From 4590b03731783664a0ef5fc7290b464c22ec2c89 Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Fri, 1 Mar 2024 16:30:50 -0800 Subject: [PATCH 01/11] WIP: initialization stable for 1 slab vacuum systems, struggling to get 2 slab systems working --- .vscode/settings.json | 3 + .../gaff.ff/ffnonbonded.itp | 2 +- parameters/mdp/energy-minimization/em.mdp | 2 +- parameters/mdp/energy-minimization/ions.mdp | 2 +- .../mdp/molecular-dynamics/npt_eqbm.mdp | 2 +- .../mdp/molecular-dynamics/npt_prod_100ns.mdp | 2 +- .../mdp/molecular-dynamics/npt_prod_500ns.mdp | 2 +- .../mdp/molecular-dynamics/nvt_eqbm.mdp | 2 +- .../mdp/molecular-dynamics/nvt_prod_100ns.mdp | 2 +- .../mdp/molecular-dynamics/nvt_prod_500ns.mdp | 2 +- scripts/method/equilibration.sh | 133 ++++++-- scripts/method/equilibration_hremd.sh | 5 +- scripts/method/index.sh | 287 ++++++++++++++++++ scripts/method/initialization.sh | 193 +----------- scripts/method/sampling_hremd.sh | 5 +- scripts/method/sampling_md.sh | 5 +- scripts/method/sampling_metadynamics.sh | 5 +- scripts/method/sampling_opes_explore.sh | 5 +- scripts/method/sampling_opes_one.sh | 5 +- ...A_0Ca_104calcite_2nm_crystal_5nm_height.sh | 2 + ...A_0Ca_104calcite_5nm_crystal_6nm_height.sh | 2 + ...2Ca_104calcite_12nm_crystal_12nm_height.sh | 2 + ...A_0Ca_104calcite_2nm_crystal_3nm_height.sh | 2 + ...A_0Ca_104calcite_1nm_crystal_3nm_height.sh | 2 + ...A_0Ca_104calcite_1nm_crystal_4nm_height.sh | 2 + ...A_0Ca_104calcite_1nm_crystal_3nm_height.sh | 2 + ...A_0Ca_104calcite_1nm_crystal_4nm_height.sh | 2 + ...A_0Ca_104calcite_2nm_crystal_4nm_height.sh | 2 + ...0Ca_104calcite_12nm_crystal_13nm_height.sh | 2 + ...2Ca_104calcite_12nm_crystal_13nm_height.sh | 2 + ...A_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ...A_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 + ...n_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 + ...c_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 + ...H_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 + ..._8Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ...16Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ...32Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + ...64Ca_104calcite_9nm_crystal_10nm_height.sh | 2 + .../1.0_104calcite_9nm_crystal_10nm_height.sh | 2 + ...aCl2_104calcite_9nm_crystal_10nm_height.sh | 2 + ...aCO3_104calcite_9nm_crystal_10nm_height.sh | 2 + ...16AA_104calcite_9nm_crystal_10nm_height.sh | 2 + ...16An_104calcite_9nm_crystal_10nm_height.sh | 2 + ...16Al_104calcite_9nm_crystal_10nm_height.sh | 2 + ...16Ac_104calcite_9nm_crystal_10nm_height.sh | 2 + .../5-one-opes-params/1.0_lowbarrier3.sh | 2 + .../5-one-opes-params/2.0_lowbarrier5.sh | 2 + .../3.0_lowbarrier5_geom370.sh | 2 + .../4.0_lowbarrier5_geom350.sh | 2 + .../5.0_lowbarrier5_lower305_geom370.sh | 2 + .../6.0_lowbarrier5_lower304_upper374.sh | 2 + .../7.0_lowbarrier8_lower304_upper374.sh | 2 + .../1.0_16paa_0Ca_9nmcrystal.sh | 2 + .../1.1_16paa_0Ca_9nmcrystal.sh | 2 + .../1.2_16paa_0Ca_9nmcrystal.sh | 2 + .../1.3_16paa_0Ca_9nmcrystal.sh | 2 + .../1.4_16paa_0Ca_9nmcrystal.sh | 2 + .../2.0_16paan_0Ca_9nmcrystal.sh | 2 + .../2.1_16paan_0Ca_9nmcrystal.sh | 2 + .../2.2_16paan_0Ca_9nmcrystal.sh | 2 + .../2.3_16paan_0Ca_9nmcrystal.sh | 2 + .../2.4_16paan_0Ca_9nmcrystal.sh | 2 + .../3.0_32paa_0Ca_12nmcrystal.sh | 2 + .../3.1_32paa_0Ca_12nmcrystal.sh | 2 + .../3.2_32paa_0Ca_12nmcrystal.sh | 2 + .../3.3_32paa_0Ca_12nmcrystal.sh | 2 + .../3.4_32paa_0Ca_12nmcrystal.sh | 2 + .../4.0_32paan_0Ca_12nmcrystal.sh | 2 + .../4.1_32paan_0Ca_12nmcrystal.sh | 2 + .../4.2_32paan_0Ca_12nmcrystal.sh | 2 + .../4.3_32paan_0Ca_12nmcrystal.sh | 2 + .../4.4_32paan_0Ca_12nmcrystal.sh | 2 + .../5.0_32paa_32CaCl2_12nmcrystal.sh | 2 + .../5.1_32paa_32CaCl2_12nmcrystal.sh | 2 + .../5.2_32paa_32CaCl2_12nmcrystal.sh | 2 + .../5.3_32paa_32CaCl2_12nmcrystal.sh | 2 + .../5.4_32paa_32CaCl2_12nmcrystal.sh | 2 + .../1.0_104calcite_9nm_crystal_10nm_height.sh | 3 +- ...aCl2_104calcite_9nm_crystal_10nm_height.sh | 2 + ...16AA_104calcite_9nm_crystal_10nm_height.sh | 2 + .../4.0_16paa_0Ca_9nmcrystal.sh | 2 + 90 files changed, 591 insertions(+), 216 deletions(-) create mode 100755 scripts/method/index.sh diff --git a/.vscode/settings.json b/.vscode/settings.json index 2167f8f..5b1366b 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,6 +4,7 @@ "arange", "aspartic", "atactic", + "atomtype", "autoscale", "avgs", "axhline", @@ -33,6 +34,7 @@ "FFTW", "fontsize", "forcefield", + "freezegrps", "Gaussians", "genion", "glutamic", @@ -135,6 +137,7 @@ "spce", "squeue", "stds", + "substr", "supercell", "tacticity", "tmax", diff --git a/force-field/eccrpa-force-fields/gaff.ff/ffnonbonded.itp b/force-field/eccrpa-force-fields/gaff.ff/ffnonbonded.itp index ce117d0..3f8d985 100644 --- a/force-field/eccrpa-force-fields/gaff.ff/ffnonbonded.itp +++ b/force-field/eccrpa-force-fields/gaff.ff/ffnonbonded.itp @@ -23,4 +23,4 @@ HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 ; SPC/E OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 ; SPC/E ; Wall atoms WR 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 ; Ficticious -WL 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 ; Ficticious +WL 0 0.0000 0.0000 A 3.16557e-01 6.50629e-01 ; Ficticious, OW_spc LJ parameters diff --git a/parameters/mdp/energy-minimization/em.mdp b/parameters/mdp/energy-minimization/em.mdp index d8d2b50..f4ca819 100644 --- a/parameters/mdp/energy-minimization/em.mdp +++ b/parameters/mdp/energy-minimization/em.mdp @@ -54,4 +54,4 @@ freezedim = Y Y Y ; directions in which the groups are f nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/energy-minimization/ions.mdp b/parameters/mdp/energy-minimization/ions.mdp index 6d0dcaf..846ca3b 100644 --- a/parameters/mdp/energy-minimization/ions.mdp +++ b/parameters/mdp/energy-minimization/ions.mdp @@ -7,7 +7,7 @@ nstcomm = 100 ; [steps] frequency for center of mass ;;; Energy minimization ;;; emtol = 10.0 ; [kJ mol^{-1} nm^{-1}] the minimization is converged when the maximum force is smaller than this value emstep = 0.10 ; [nm] initial step-size -nsteps = 100000 ; [steps] Maximum number of (minimization) steps to perform +nsteps = 10000 ; [steps] Maximum number of (minimization) steps to perform ;;; Output control ;;; nstxout = 0 ; [steps] number of steps that elapse between writing coordinates to the output trajectory file (trr) nstvout = 0 ; [steps] number of steps that elapse between writing velocities to the output trajectory file (trr) diff --git a/parameters/mdp/molecular-dynamics/npt_eqbm.mdp b/parameters/mdp/molecular-dynamics/npt_eqbm.mdp index c42eee8..8871727 100644 --- a/parameters/mdp/molecular-dynamics/npt_eqbm.mdp +++ b/parameters/mdp/molecular-dynamics/npt_eqbm.mdp @@ -59,4 +59,4 @@ lincs-warnangle = 30 ; print warning to log file and stderr nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/molecular-dynamics/npt_prod_100ns.mdp b/parameters/mdp/molecular-dynamics/npt_prod_100ns.mdp index 389954c..53b5a34 100644 --- a/parameters/mdp/molecular-dynamics/npt_prod_100ns.mdp +++ b/parameters/mdp/molecular-dynamics/npt_prod_100ns.mdp @@ -58,4 +58,4 @@ lincs-warnangle = 30 ; print warning to log file and stderr nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/molecular-dynamics/npt_prod_500ns.mdp b/parameters/mdp/molecular-dynamics/npt_prod_500ns.mdp index bf127cb..add102f 100644 --- a/parameters/mdp/molecular-dynamics/npt_prod_500ns.mdp +++ b/parameters/mdp/molecular-dynamics/npt_prod_500ns.mdp @@ -58,4 +58,4 @@ lincs-warnangle = 30 ; print warning to log file and stderr nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/molecular-dynamics/nvt_eqbm.mdp b/parameters/mdp/molecular-dynamics/nvt_eqbm.mdp index 11c5adb..6172afc 100644 --- a/parameters/mdp/molecular-dynamics/nvt_eqbm.mdp +++ b/parameters/mdp/molecular-dynamics/nvt_eqbm.mdp @@ -57,4 +57,4 @@ freezedim = Y Y Y ; directions in which the groups are fr nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp b/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp index 7bb6d3c..56965c4 100644 --- a/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp +++ b/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp @@ -57,4 +57,4 @@ freezedim = Y Y Y ; directions in which the groups are fr nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp b/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp index da507a2..3ce9e76 100644 --- a/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp +++ b/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp @@ -57,4 +57,4 @@ freezedim = Y Y Y ; directions in which the groups are fr nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential wall-atomtype = WR WL ; the atom type name in the force field for each wall. -wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 772e8b5..965bc4a 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -85,8 +85,10 @@ else cp -np "${previous_archive_dir}/topol.top" "topol.top" || exit 1 cp -np "${previous_archive_dir}/index.ndx" "index.ndx" || exit 1 - # replace temperature in mdp file cp "${mdp_file_nvt}" "${sim_name}.mdp" || exit 1 + # freeze atoms in mdp file + sed -i 's/freezegrps.*/freezegrps = Crystal/g' "${sim_name}.mdp" || exit 1 + # replace temperature in mdp file sed -i 's/ref-t.*/ref-t = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 # small surfaces have smaller cutoffs @@ -95,6 +97,12 @@ else sed -i 's/^rcoulomb.*/rcoulomb = 0.7/g' "${sim_name}.mdp" || exit 1 sed -i 's/^rvdw.*/rvdw = 0.7/g' "${sim_name}.mdp" || exit 1 fi + # add vacuum parameters to mdp file + if [[ "${VACUUM}" == 'True' ]]; then + sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 + sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 + sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + fi # make tpr file for NVT equilibration "${GMX_BIN}" -nocopyright grompp \ @@ -176,8 +184,10 @@ else # copy output files from NVT equilibration cp -np "${previous_archive_dir}/${previous_sim_name}.gro" "${previous_sim_name}.gro" || exit 1 - # replace temperature and pressure in mdp file cp "${mdp_file_npt}" "${sim_name}.mdp" || exit 1 + # freeze atoms in mdp file + sed -i 's/freezegrps.*/freezegrps = Crystal/g' "${sim_name}.mdp" || exit 1 + # replace temperature and pressure in mdp file sed -i 's/ref-t.*/ref-t = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/ref-p.*/ref-p = '"${PRESSURE_BAR} ${PRESSURE_BAR}/g" "${sim_name}.mdp" || exit 1 @@ -187,6 +197,12 @@ else sed -i 's/^rcoulomb.*/rcoulomb = 0.7/g' "${sim_name}.mdp" || exit 1 sed -i 's/^rvdw.*/rvdw = 0.7/g' "${sim_name}.mdp" || exit 1 fi + # add vacuum parameters to mdp file + if [[ "${VACUUM}" == 'True' ]]; then + sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 + sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 + sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + fi # make tpr file "${GMX_BIN}" -nocopyright grompp \ @@ -279,24 +295,100 @@ for i in "${!previous_sim_gro_box_dimensions_array[@]}"; do echo "DEBUG: Percent change in dimension ${i}: ${percent_change}"'%' done -# ############################################################################## -# Add Vacuum Layer ############################################################# -# ############################################################################## -if [[ "${VACUUM_HEIGHT}" -eq 0 ]]; then - echo "INFO: Skipping vacuum layer" -else - echo "INFO: Adding vacuum layer" - { - # get box height from last line of gro file - box_dim="$(tail -n 1 "${sim_name}.gro")" - z_height="$(echo "${box_dim}" | awk '{print $3}')" - z_vacuum_height="$(bc <<<"scale=5; ${z_height} + ${VACUUM_HEIGHT}")" - - # replace z-dimension of box with vacuum layer by string replacement of 3rd column in last line of gro file - sed -i "s/${z_height}/${z_vacuum_height}/g" "${sim_name}.gro" - } >>"${log_file}" 2>&1 +# ####################################################################################### +# Add Second Slab ###################################################################### +# ####################################################################################### +z_buffer='0.2' + +if [[ "${N_SLAB}" -eq 2 ]]; then + echo "INFO: Adding second slab" + + # check if output gro file already exists + if [[ -f "${sim_name}_2slab.gro" ]]; then + echo "DEBUG: Second slab already added" + else + { + # copy crystal.pdb from initialization + cp -np "../1-energy-minimization/crystal.gro" "crystal.gro" || exit 1 + + # find maximum z-coordinate of box from previous gro file + box_dim="$(tail -n 1 "${archive_dir}/${sim_name}.gro")" + z_height="$(echo "${box_dim}" | awk '{print $3}')" + + # calculate z-height of crystal and move slab to desired position + z_coords="$(awk 'NR>2 {print $6}' "crystal.gro")" + z_coords="$(echo "${z_coords}" | head -n -1 | sort -n)" + z_max="$(echo "${z_coords}" | tail -n 1)" + z_min="$(echo "${z_coords}" | head -n 1)" + z_height_crystal="$(echo "scale=5; ${z_max} - ${z_min}" | bc)" + z_translate="$(echo "scale=5; ${z_height} + ${z_max}" | bc)" + z_height_2slab="$(echo "scale=5; ${z_height} + ${z_height_crystal} + ${z_buffer}" | bc)" + + # insert "-" at column 39 in all lines of gro file to reflect crystal on z-axis + awk '{print substr($0,1,38)"-"substr($0,40)}' "crystal.gro" >"crystal_reflected.gro" + head -n 2 crystal.gro >temp.txt + tail -n +3 crystal_reflected.gro >>temp.txt + head -n -1 temp.txt >temp2.txt + mv temp2.txt temp.txt + tail -n 1 crystal.gro >>temp.txt + mv temp.txt crystal_reflected.gro + + # move reflected crystal to top of box + "${GMX_BIN}" editconf \ + -f "crystal_reflected.gro" \ + -o "crystal_reflected.gro" \ + -translate 0 0 "${z_translate}" + + # get crystal coordinates for a dat file + z_cryst="$(awk 'NR>2 {print $6}' "crystal_reflected.gro")" + z_cryst="$(echo "${z_cryst}" | head -n -1)" + y_cryst="$(awk 'NR>2 {print $5}' "crystal_reflected.gro")" + y_cryst="$(echo "${y_cryst}" | head -n -1)" + x_cryst="$(awk 'NR>2 {print $4}' "crystal_reflected.gro")" + x_cryst="$(echo "${x_cryst}" | head -n -1)" + paste <(echo "${x_cryst}") <(echo "${y_cryst}") <(echo "${z_cryst}") >positions.dat + + # increase box size in z-dimension by z_height_crystal + cp -np "${archive_dir}/${sim_name}.gro" "${sim_name}_2slab_pre.gro" || exit 1 + sed -i "s/${z_height}/${z_height_2slab}/" "${sim_name}_2slab_pre.gro" + + # FIXME: this is not working + # insert reflected crystal into gro file + "${GMX_BIN}" insert-molecules \ + -f "${sim_name}_2slab_pre.gro" \ + -ci "crystal_reflected.gro" \ + -ip "positions.dat" \ + -rot 'none' \ + -radius '0' \ + -dr '0' '0' '1' \ + -replace 'SOL' \ + -o "${sim_name}_2slab.gro" || exit 1 + + # TODO: add second slab to simulation + + # TODO: update index file + + } >>"${log_file}" 2>&1 + fi + + echo "DEBUG: Crystal height: ${z_height_crystal}" fi +# ####################################################################################### +# Make box orthorhombic ############################################################## +# ####################################################################################### +echo "INFO: Making box orthorhombic" +{ + cp -np "${archive_dir}/${sim_name}.gro" "${archive_dir}/${sim_name}_triclinic.gro" + "${GMX_BIN}" trjconv \ + -f "${archive_dir}/${sim_name}.gro" \ + -s "${archive_dir}/${sim_name}.tpr" \ + -o "${archive_dir}/${sim_name}.gro" \ + -ur 'rect' <>"${log_file}" 2>&1 + # ####################################################################################### # Production equilibration ############################################################## # ####################################################################################### @@ -330,10 +422,13 @@ else sed -i 's/^rvdw.*/rvdw = 0.7/g' "${sim_name}.mdp" || exit 1 fi # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # copy plumed file diff --git a/scripts/method/equilibration_hremd.sh b/scripts/method/equilibration_hremd.sh index e4b67c8..bc3c87a 100755 --- a/scripts/method/equilibration_hremd.sh +++ b/scripts/method/equilibration_hremd.sh @@ -135,10 +135,13 @@ else sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/ref-p.*/ref-p = '"${PRESSURE_BAR} ${PRESSURE_BAR}/g" "${sim_name}.mdp" || exit 1 # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # copy plumed file diff --git a/scripts/method/index.sh b/scripts/method/index.sh new file mode 100755 index 0000000..e848afb --- /dev/null +++ b/scripts/method/index.sh @@ -0,0 +1,287 @@ +#!/usr/bin/env bash +# -*- coding: utf-8 -*- +# +# Author : Alec Glisman (GitHub: @alec-glisman) +# Date : 2024-03-01 +# Description: Script to create initial system for MD simulations +# Usage : ./index.sh +# Notes : Script assumes that global variables have been set in a +# submission/input/*.sh script. Script should only be called from +# the initialization.sh script. + +log_file="index.log" +sim_name="energy_minimization" + +# ############################################################################## +# Make Default Index File ###################################################### +# ############################################################################## +echo "INFO: Making default index file" | tee -a "${log_file}" + +{ + # create blank index file + if [[ "${N_CHAIN}" -gt 0 ]]; then + idx_group='17' + else + idx_group='6' + fi + + "${GMX_BIN}" make_ndx \ + -f "${sim_name}.gro" \ + -o "index.ndx" \ + <"index_crystal.ndx" || true +} >>"${log_file}" 2>&1 + +# ############################################################################## +# Polymer Groups to Index File ################################################# +# ############################################################################## +if [[ "${N_CHAIN}" -gt 0 ]]; then + echo "INFO: Adding polymer groups to index file" | tee -a "${log_file}" + { + "${GMX_BIN}" make_ndx \ + -f "pdb2gmx_clean.pdb" \ + -n "index.ndx" \ + -o "index.ndx" \ + <>"${log_file}" 2>&1 +fi + +# ############################################################################## +# Add Ion Groups to Index File ################################################# +# ############################################################################## +echo "INFO: Adding ion groups to index file" | tee -a "${log_file}" +{ + # add aqueous sodium ions to index file + if [[ "${N_SODIUM}" -gt 0 ]]; then + "${GMX_BIN}" make_ndx \ + -f "${sim_name}.pdb" \ + -n "index.ndx" \ + -o "index.ndx" \ + <>"${log_file}" 2>&1 + +# ############################################################################## +# 3D PBC ####################################################################### +# ############################################################################## +if [[ "${VACUUM}" == "False" ]]; then + echo "INFO: Adding 3D PBC groups to index file" | tee -a "${log_file}" + { + "${GMX_BIN}" select \ + -f "crystal.pdb" \ + -s "crystal.pdb" \ + -n "index.ndx" \ + -on "index_crystal.ndx" \ + <= ${PDB_BULK_ZMIN} and z <= ${PDB_BULK_ZMAX})) +"Crystal_Top_Surface" same residue as (name CX1 CA and (z > ${PDB_BULK_ZMAX})) +"Crystal_Bottom_Surface" same residue as (name CX1 CA and (z < ${PDB_BULK_ZMIN})) +EOF + # save group numbers + group_crystal="${idx_group}" + group_bulk="$((idx_group + 1))" + group_top_surface="$((idx_group + 2))" + group_bottom_surface="$((idx_group + 3))" + + # remove "f0_t0.000" from index file groups + sed -i 's/_f0_t0.000//g' "index_crystal.ndx" + # append crystal groups to index file + cat "index_crystal.ndx" >>"index.ndx" + idx_group=$((idx_group + 4)) + + # add crystal sub-groups to index file + "${GMX_BIN}" make_ndx \ + -f "crystal.pdb" \ + -n "index.ndx" \ + -o "index.ndx" \ + <>"${log_file}" 2>&1 +fi + +# ############################################################################## +# 2D PBC ####################################################################### +# ############################################################################## +if [[ "${VACUUM}" == "True" ]]; then + echo "INFO: Adding 2D PBC groups to index file" | tee -a "${log_file}" + { + "${GMX_BIN}" select \ + -f "crystal.pdb" \ + -s "crystal.pdb" \ + -n "index.ndx" \ + -on "index_crystal.ndx" \ + < ${PDB_BULK_ZMAX})) +EOF + # save group numbers + group_crystal="${idx_group}" + group_bulk="$((idx_group + 1))" + group_top_surface="$((idx_group + 2))" + + # remove "f0_t0.000" from index file groups + sed -i 's/_f0_t0.000//g' "index_crystal.ndx" + # append crystal groups to index file + cat "index_crystal.ndx" >>"index.ndx" + idx_group=$((idx_group + 3)) + + # add crystal sub-groups to index file + "${GMX_BIN}" make_ndx \ + -f "crystal.pdb" \ + -n "index.ndx" \ + -o "index.ndx" \ + <>"${log_file}" 2>&1 +fi diff --git a/scripts/method/initialization.sh b/scripts/method/initialization.sh index e6bdbd0..4cb8289 100755 --- a/scripts/method/initialization.sh +++ b/scripts/method/initialization.sh @@ -106,6 +106,12 @@ echo "INFO: Copying input files to working directory" sed -i 's/^rcoulomb.*/rcoulomb = 0.7/g' "mdin.mdp" sed -i 's/^rvdw.*/rvdw = 0.7/g' "mdin.mdp" fi + # add vacuum parameters to mdp file + if [[ "${VACUUM}" == "True" ]]; then + sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "mdin.mdp" + sed -i 's/^pbc .*/pbc = xy/g' "mdin.mdp" + sed -i 's/^nwall .*/nwall = 2/g' "mdin.mdp" + fi } >>"${log_file}" 2>&1 # ############################################################################## @@ -177,7 +183,7 @@ echo "INFO: Importing structure to Gromacs" minimum_z_coord="$(echo "${carbonate_carbon_z}" | sort -n)" z_min="$(echo "${minimum_z_coord}" | awk 'NR==1{print $1}')" # subtract offset [nm] to z_min to ensure that all atoms are within the box and we can see water structure - offset='0.05' + offset='0.00' z_min="$(bc <<<"scale=5; ${z_min} - ${offset}")" echo "DEBUG: Minimum z-coordinate of crystal [nm]: ${z_min}" @@ -215,7 +221,7 @@ echo "INFO: Adding solvent" # subtract z_min from pdb bulk z-coordinates and add buffer for outer layers buffer='0.3' - gro_zmin="$(bc <<<"scale=5; ${PDB_BULK_ZMIN} - ${z_min} - ${buffer}")" + # gro_zmin="$(bc <<<"scale=5; ${PDB_BULK_ZMIN} - ${z_min} - ${buffer}")" gro_zmax="$(bc <<<"scale=5; ${PDB_BULK_ZMAX} - ${z_min} + ${buffer}")" # find "bad" water molecules that are inside the crystal @@ -223,7 +229,7 @@ echo "INFO: Adding solvent" -f "${sim_name}.gro" \ -s "${sim_name}.gro" \ -on "bad_waters.ndx" <= ${gro_zmin} and z <= ${gro_zmax})) +"Bad_SOL" same residue as (name OW HW1 HW2 and (z <= ${gro_zmax})) EOF # remove "f0_t0.000" from index file groups sed -i 's/_f0_t0.000//g' "bad_waters.ndx" @@ -249,7 +255,7 @@ Good_Atoms EOF } >>"${log_file}" 2>&1 -echo "DEBUG: Minimum z-coordinate of crystal after solvation [nm]: ${gro_zmin}" +# echo "DEBUG: Minimum z-coordinate of crystal after solvation [nm]: ${gro_zmin}" echo "DEBUG: Maximum z-coordinate of crystal after solvation [nm]: ${gro_zmax}" # find number of "bad" water molecules from log file @@ -377,183 +383,8 @@ EOF # ############################################################################## # Make Index File ############################################################## # ############################################################################## -echo "INFO: Making index file" -{ - # create blank index file - if [[ "${N_CHAIN}" -gt 0 ]]; then - idx_group='17' - else - idx_group='6' - fi - idx_crystal="${idx_group}" - - "${GMX_BIN}" make_ndx \ - -f "${sim_name}.gro" \ - -o "index.ndx" \ - <"index_crystal.ndx" || true - - # add crystal groups to index file - "${GMX_BIN}" select \ - -f "crystal.pdb" \ - -s "crystal.pdb" \ - -n "index.ndx" \ - -on "index_crystal.ndx" \ - <= ${PDB_BULK_ZMIN} and z <= ${PDB_BULK_ZMAX})) -"Top_Crystal_Surface" same residue as (name CX1 CA and (z > ${PDB_BULK_ZMAX})) -"Bottom_Crystal_Surface" same residue as (name CX1 CA and (z < ${PDB_BULK_ZMIN})) -EOF - # save group numbers - group_bulk="$((idx_group + 1))" - group_top_surface="$((idx_group + 2))" - group_bottom_surface="$((idx_group + 3))" - - # remove "f0_t0.000" from index file groups - sed -i 's/_f0_t0.000//g' "index_crystal.ndx" - # append crystal groups to index file - cat "index_crystal.ndx" >>"index.ndx" - idx_group=$((idx_group + 4)) - - # add crystal sub-groups to index file - "${GMX_BIN}" make_ndx \ - -f "crystal.pdb" \ - -n "index.ndx" \ - -o "index.ndx" \ - <>"${log_file}" 2>&1 +echo "INFO: Calling index.sh" +"${script_path}/index.sh" # ############################################################################## # Add positional restraints #################################################### diff --git a/scripts/method/sampling_hremd.sh b/scripts/method/sampling_hremd.sh index ffd3a67..9e0bc31 100755 --- a/scripts/method/sampling_hremd.sh +++ b/scripts/method/sampling_hremd.sh @@ -122,10 +122,13 @@ else sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/ref-p.*/ref-p = '"${PRESSURE_BAR} ${PRESSURE_BAR}/g" "${sim_name}.mdp" || exit 1 # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # non-base replicas write data 10x less frequently if [[ "${replica}" -ne '00' ]]; then diff --git a/scripts/method/sampling_md.sh b/scripts/method/sampling_md.sh index 834fc73..032e41f 100755 --- a/scripts/method/sampling_md.sh +++ b/scripts/method/sampling_md.sh @@ -103,10 +103,13 @@ else sed -i 's/^rvdw.*/rvdw = 0.7/g' "${sim_name}.mdp" || exit 1 fi # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # create tpr file diff --git a/scripts/method/sampling_metadynamics.sh b/scripts/method/sampling_metadynamics.sh index cc9a987..a227e3e 100755 --- a/scripts/method/sampling_metadynamics.sh +++ b/scripts/method/sampling_metadynamics.sh @@ -96,10 +96,13 @@ else sed -i 's/^rvdw.*/rvdw = 0.7/g' "${sim_name}.mdp" || exit 1 fi # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # copy plumed file diff --git a/scripts/method/sampling_opes_explore.sh b/scripts/method/sampling_opes_explore.sh index d14d759..3c2dcb7 100755 --- a/scripts/method/sampling_opes_explore.sh +++ b/scripts/method/sampling_opes_explore.sh @@ -90,10 +90,13 @@ else sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/ref-p.*/ref-p = '"${PRESSURE_BAR} ${PRESSURE_BAR}/g" "${sim_name}.mdp" || exit 1 # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # copy plumed file diff --git a/scripts/method/sampling_opes_one.sh b/scripts/method/sampling_opes_one.sh index a59d076..9050909 100755 --- a/scripts/method/sampling_opes_one.sh +++ b/scripts/method/sampling_opes_one.sh @@ -106,10 +106,13 @@ sim_name="prod_opes_one_multicv" sed -i 's/nstenergy.*/nstenergy = 10000/g' "${sim_name}.mdp" || exit 1 fi # add vacuum parameters to mdp file - if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then + if [[ "${VACUUM}" == 'True' ]]; then sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + if [[ "${N_SLABS}" -eq 2 ]]; then + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 + fi fi # copy plumed file diff --git a/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh b/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh index 48c4e42..116fede 100755 --- a/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh +++ b/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='2' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='5' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh b/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh index 18f1238..d8cef03 100755 --- a/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh +++ b/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='5' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='6' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='8' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh b/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh index 45cc465..a1de02e 100755 --- a/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh +++ b/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='12' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh index daf951e..2e170de 100755 --- a/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='2' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='2' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='3' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh index 1490bec..c02bb34 100755 --- a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='1' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='3' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='3' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh index c466f8a..176777b 100755 --- a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='1' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='4' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='3' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh index 82757ff..cdc3202 100755 --- a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='1' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='3' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='4' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh index f5ba803..bbb02e1 100755 --- a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='1' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='4' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='4' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh index 5d596ac..86ab381 100755 --- a/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='2' # size of crystal surface in nm {1, 2, 3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='3' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='4' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh b/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh index 3d42811..86ebc43 100755 --- a/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh +++ b/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh @@ -17,6 +17,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -24,6 +25,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh b/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh index ece53b9..c73c5e6 100755 --- a/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh +++ b/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh @@ -17,6 +17,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -24,6 +25,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh index c49d557..d8a0321 100755 --- a/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -17,6 +17,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='5' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='8' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -24,6 +25,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='8' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 9b3797f..85002ed 100755 --- a/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 2a6346a..2ccabf0 100755 --- a/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 7323df2..1b11f94 100755 --- a/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 9ef7c78..d6481d3 100755 --- a/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 3f479b7..fccf2ff 100755 --- a/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh index 0276784..01df74a 100755 --- a/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh index 00cb420..6e26ba2 100755 --- a/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh index 389a4b4..ebb39e7 100755 --- a/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh index 6dbddfb..6f0b868 100755 --- a/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='5' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='8' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh index 6ac9b9a..2dd166e 100755 --- a/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='5' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='8' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh index ca1d1b0..658a70e 100755 --- a/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='5' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='8' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh index 826209c..1c153b9 100755 --- a/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='5' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='8' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh index 8c4c20c..1b57a09 100755 --- a/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh index c063451..50b7873 100755 --- a/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh index 33f9e9a..b15192e 100755 --- a/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh index 7868ed7..1524266 100755 --- a/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 5504313..3f6f190 100755 --- a/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index 61e832e..7ed9b31 100755 --- a/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh index b51d8b6..b11c92d 100755 --- a/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='64' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh index 68d6099..da6f622 100755 --- a/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh index c0bff0f..678f01b 100755 --- a/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh index 72a6a86..0fc8db9 100755 --- a/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh index 8fe8332..dd8c6be 100755 --- a/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/1.0_lowbarrier3.sh b/submission/input/5-one-opes-params/1.0_lowbarrier3.sh index 1cbd6c5..58eeb8b 100755 --- a/submission/input/5-one-opes-params/1.0_lowbarrier3.sh +++ b/submission/input/5-one-opes-params/1.0_lowbarrier3.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/2.0_lowbarrier5.sh b/submission/input/5-one-opes-params/2.0_lowbarrier5.sh index 25111df..682be25 100755 --- a/submission/input/5-one-opes-params/2.0_lowbarrier5.sh +++ b/submission/input/5-one-opes-params/2.0_lowbarrier5.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh b/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh index 13bf00c..5c0606f 100755 --- a/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh +++ b/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh b/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh index d8c6894..2487df5 100755 --- a/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh +++ b/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh b/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh index 5a713ae..e31bc6c 100755 --- a/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh +++ b/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh b/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh index 1002f71..cbe7649 100755 --- a/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh +++ b/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh b/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh index 4d8fdcc..697cc9f 100755 --- a/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh +++ b/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh @@ -31,6 +31,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -38,6 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh index 2b8146c..9005c04 100755 --- a/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh index a1940b3..1486864 100755 --- a/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh index bf4e7b0..a480ded 100755 --- a/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh index c85641d..46d9cfd 100755 --- a/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh index 4954b20..ad0e445 100755 --- a/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh index a8a60eb..a6808c2 100755 --- a/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh index a7102bc..7cf0446 100755 --- a/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh index 8694140..b6c1717 100755 --- a/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh index 0104dd9..2c2d069 100755 --- a/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh index 4d90414..fa71f1f 100755 --- a/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh index f079aa1..47e7ed2 100755 --- a/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh index ded9d8b..1ab91ee 100755 --- a/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh index 1e3d749..ca080e2 100755 --- a/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh index 275572c..1573020 100755 --- a/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh index ead3a9a..25126e7 100755 --- a/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh index cc78ece..d90153e 100755 --- a/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh index 0a6618e..a8498f4 100755 --- a/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh index b4cc635..7fb323b 100755 --- a/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh index 35b9e86..23f3831 100755 --- a/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh index 090d094..4a65168 100755 --- a/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh index 5b7d65b..868bd20 100755 --- a/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh index d039243..ef73588 100755 --- a/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh index 11c80d7..2f97c34 100755 --- a/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh index 506748e..a0b84ae 100755 --- a/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh index e7bfbc8..015ea6d 100755 --- a/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='False' # {True, False} export SURFACE_SIZE='12' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='13' # height of simulation box in nm export VACUUM_HEIGHT='0' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 98dce43..55cbc64 100755 --- a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -34,13 +34,14 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='True' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm -export VACUUM_HEIGHT='30' # height of vacuum layer in nm export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in nm in PDB file export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index 51cde50..8d48068 100755 --- a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='True' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='30' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh index aa4b667..a212a0c 100755 --- a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='True' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='30' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh index 69521db..36cedfa 100755 --- a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh @@ -34,6 +34,7 @@ export CRYSTAL="calcite" # {calcite, aragonite, vaterite} export SURFACE="104" # Miller index of crystal surface {104, 001} # system size +export VACUUM='True' # {True, False} export SURFACE_SIZE='9' # size of crystal surface in nm {3, 5, 8, 9, 10, 11, 12, 13} export BOX_HEIGHT='10' # height of simulation box in nm export VACUUM_HEIGHT='30' # height of vacuum layer in nm @@ -41,6 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component +export N_SLABS='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions From a9648b3ca4cfab5907e66cf3d775fa75c8dfd989 Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Fri, 1 Mar 2024 16:49:50 -0800 Subject: [PATCH 02/11] 2slab creation stable, need to update topology --- scripts/method/equilibration.sh | 32 ++++++++++++++++++++------------ 1 file changed, 20 insertions(+), 12 deletions(-) diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 965bc4a..69df19d 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -352,21 +352,29 @@ if [[ "${N_SLAB}" -eq 2 ]]; then cp -np "${archive_dir}/${sim_name}.gro" "${sim_name}_2slab_pre.gro" || exit 1 sed -i "s/${z_height}/${z_height_2slab}/" "${sim_name}_2slab_pre.gro" - # FIXME: this is not working - # insert reflected crystal into gro file - "${GMX_BIN}" insert-molecules \ + # convert box and crystal to pdb files + "${GMX_BIN}" editconf \ -f "${sim_name}_2slab_pre.gro" \ - -ci "crystal_reflected.gro" \ - -ip "positions.dat" \ - -rot 'none' \ - -radius '0' \ - -dr '0' '0' '1' \ - -replace 'SOL' \ - -o "${sim_name}_2slab.gro" || exit 1 + -o "${sim_name}_2slab_pre.pdb" + sed -i '/^TER/d' "${sim_name}_2slab_pre.pdb" + sed -i '/^ENDMDL/d' "${sim_name}_2slab_pre.pdb" + "${GMX_BIN}" editconf \ + -f "crystal_reflected.gro" \ + -o "crystal_reflected.pdb" + sed -i "/^TITLE.*/d" "crystal_reflected.pdb" + sed -i "/^REMARK.*/d" "crystal_reflected.pdb" + sed -i "/^CRYST1.*/d" "crystal_reflected.pdb" + sed -i "/^MODEL.*/d" "crystal_reflected.pdb" + + # merge pdb files into gro file + \cat "${sim_name}_2slab_pre.pdb" "crystal_reflected.pdb" >"${sim_name}_2slab.pdb" + "${GMX_BIN}" editconf \ + -f "${sim_name}_2slab.pdb" \ + -o "${sim_name}_2slab.gro" - # TODO: add second slab to simulation + # TODO: make new topology files with 2slab - # TODO: update index file + # TODO: make new index file } >>"${log_file}" 2>&1 fi From e30b425a43ebbc7fe356c133d5cff65296196f5a Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:44:24 -0800 Subject: [PATCH 03/11] using two "real" walls on all vacuum EM and first two EQBM --- .vscode/settings.json | 1 + scripts/method/equilibration.sh | 87 ++------------------- scripts/method/initialization.sh | 5 +- scripts/{method => utilities}/index.sh | 0 scripts/utilities/second_slab.sh | 103 +++++++++++++++++++++++++ 5 files changed, 114 insertions(+), 82 deletions(-) rename scripts/{method => utilities}/index.sh (100%) create mode 100755 scripts/utilities/second_slab.sh diff --git a/.vscode/settings.json b/.vscode/settings.json index 5b1366b..ce2049a 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -28,6 +28,7 @@ "DREGRESSIONTEST", "eccrpa", "editconf", + "ENDMDL", "eneconv", "eqbm", "ewald", diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 69df19d..8391f0b 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -102,6 +102,8 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 + echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 fi # make tpr file for NVT equilibration @@ -202,6 +204,8 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 + echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 fi # make tpr file @@ -298,88 +302,11 @@ done # ####################################################################################### # Add Second Slab ###################################################################### # ####################################################################################### -z_buffer='0.2' - if [[ "${N_SLAB}" -eq 2 ]]; then echo "INFO: Adding second slab" - - # check if output gro file already exists - if [[ -f "${sim_name}_2slab.gro" ]]; then - echo "DEBUG: Second slab already added" - else - { - # copy crystal.pdb from initialization - cp -np "../1-energy-minimization/crystal.gro" "crystal.gro" || exit 1 - - # find maximum z-coordinate of box from previous gro file - box_dim="$(tail -n 1 "${archive_dir}/${sim_name}.gro")" - z_height="$(echo "${box_dim}" | awk '{print $3}')" - - # calculate z-height of crystal and move slab to desired position - z_coords="$(awk 'NR>2 {print $6}' "crystal.gro")" - z_coords="$(echo "${z_coords}" | head -n -1 | sort -n)" - z_max="$(echo "${z_coords}" | tail -n 1)" - z_min="$(echo "${z_coords}" | head -n 1)" - z_height_crystal="$(echo "scale=5; ${z_max} - ${z_min}" | bc)" - z_translate="$(echo "scale=5; ${z_height} + ${z_max}" | bc)" - z_height_2slab="$(echo "scale=5; ${z_height} + ${z_height_crystal} + ${z_buffer}" | bc)" - - # insert "-" at column 39 in all lines of gro file to reflect crystal on z-axis - awk '{print substr($0,1,38)"-"substr($0,40)}' "crystal.gro" >"crystal_reflected.gro" - head -n 2 crystal.gro >temp.txt - tail -n +3 crystal_reflected.gro >>temp.txt - head -n -1 temp.txt >temp2.txt - mv temp2.txt temp.txt - tail -n 1 crystal.gro >>temp.txt - mv temp.txt crystal_reflected.gro - - # move reflected crystal to top of box - "${GMX_BIN}" editconf \ - -f "crystal_reflected.gro" \ - -o "crystal_reflected.gro" \ - -translate 0 0 "${z_translate}" - - # get crystal coordinates for a dat file - z_cryst="$(awk 'NR>2 {print $6}' "crystal_reflected.gro")" - z_cryst="$(echo "${z_cryst}" | head -n -1)" - y_cryst="$(awk 'NR>2 {print $5}' "crystal_reflected.gro")" - y_cryst="$(echo "${y_cryst}" | head -n -1)" - x_cryst="$(awk 'NR>2 {print $4}' "crystal_reflected.gro")" - x_cryst="$(echo "${x_cryst}" | head -n -1)" - paste <(echo "${x_cryst}") <(echo "${y_cryst}") <(echo "${z_cryst}") >positions.dat - - # increase box size in z-dimension by z_height_crystal - cp -np "${archive_dir}/${sim_name}.gro" "${sim_name}_2slab_pre.gro" || exit 1 - sed -i "s/${z_height}/${z_height_2slab}/" "${sim_name}_2slab_pre.gro" - - # convert box and crystal to pdb files - "${GMX_BIN}" editconf \ - -f "${sim_name}_2slab_pre.gro" \ - -o "${sim_name}_2slab_pre.pdb" - sed -i '/^TER/d' "${sim_name}_2slab_pre.pdb" - sed -i '/^ENDMDL/d' "${sim_name}_2slab_pre.pdb" - "${GMX_BIN}" editconf \ - -f "crystal_reflected.gro" \ - -o "crystal_reflected.pdb" - sed -i "/^TITLE.*/d" "crystal_reflected.pdb" - sed -i "/^REMARK.*/d" "crystal_reflected.pdb" - sed -i "/^CRYST1.*/d" "crystal_reflected.pdb" - sed -i "/^MODEL.*/d" "crystal_reflected.pdb" - - # merge pdb files into gro file - \cat "${sim_name}_2slab_pre.pdb" "crystal_reflected.pdb" >"${sim_name}_2slab.pdb" - "${GMX_BIN}" editconf \ - -f "${sim_name}_2slab.pdb" \ - -o "${sim_name}_2slab.gro" - - # TODO: make new topology files with 2slab - - # TODO: make new index file - - } >>"${log_file}" 2>&1 - fi - - echo "DEBUG: Crystal height: ${z_height_crystal}" + cp -np "${archive_dir}/${sim_name}.gro" "${sim_name}.gro" + "${project_path}/scripts/utilities/second_slab.sh" || exit 1 + rm "${sim_name}.gro" fi # ####################################################################################### diff --git a/scripts/method/initialization.sh b/scripts/method/initialization.sh index 4cb8289..37ac99a 100755 --- a/scripts/method/initialization.sh +++ b/scripts/method/initialization.sh @@ -111,6 +111,7 @@ echo "INFO: Copying input files to working directory" sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "mdin.mdp" sed -i 's/^pbc .*/pbc = xy/g' "mdin.mdp" sed -i 's/^nwall .*/nwall = 2/g' "mdin.mdp" + sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "mdin.mdp" fi } >>"${log_file}" 2>&1 @@ -183,7 +184,7 @@ echo "INFO: Importing structure to Gromacs" minimum_z_coord="$(echo "${carbonate_carbon_z}" | sort -n)" z_min="$(echo "${minimum_z_coord}" | awk 'NR==1{print $1}')" # subtract offset [nm] to z_min to ensure that all atoms are within the box and we can see water structure - offset='0.00' + offset='0.1' z_min="$(bc <<<"scale=5; ${z_min} - ${offset}")" echo "DEBUG: Minimum z-coordinate of crystal [nm]: ${z_min}" @@ -384,7 +385,7 @@ EOF # Make Index File ############################################################## # ############################################################################## echo "INFO: Calling index.sh" -"${script_path}/index.sh" +"${project_path}/scripts/utilities/index.sh" || exit 1 # ############################################################################## # Add positional restraints #################################################### diff --git a/scripts/method/index.sh b/scripts/utilities/index.sh similarity index 100% rename from scripts/method/index.sh rename to scripts/utilities/index.sh diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh new file mode 100755 index 0000000..0455d2a --- /dev/null +++ b/scripts/utilities/second_slab.sh @@ -0,0 +1,103 @@ +#!/usr/bin/env bash +# -*- coding: utf-8 -*- +# +# Author : Alec Glisman (GitHub: @alec-glisman) +# Date : 2024-03-04 +# Description: Script to create initial system for MD simulations +# Usage : ./second_slab.sh +# Notes : Script assumes that global variables have been set in a +# submission/input/*.sh script. Script should only be called from +# the equilibration.sh script. + +z_buffer="0.1" # [nm] +sim_name="npt_eqbm" +archive_dir="3-second-slab" +log_file="second_slab.log" + +# ############################################################################## +# Add second slab to box ####################################################### +# ############################################################################## +# check if output gro file already exists +if [[ -f "${sim_name}_2slab.gro" ]]; then + echo "DEBUG: Second slab already added" +else + { + # copy crystal.pdb from initialization + cp -np "../1-energy-minimization/crystal.gro" "crystal.gro" || exit 1 + + # find maximum z-coordinate of box from previous gro file + box_dim="$(tail -n 1 "${sim_name}.gro")" + z_height="$(echo "${box_dim}" | awk '{print $3}')" + + # calculate z-height of crystal and move slab to desired position + z_coords="$(awk 'NR>2 {print $6}' "crystal.gro")" + z_coords="$(echo "${z_coords}" | head -n -1 | sort -n)" + z_max="$(echo "${z_coords}" | tail -n 1)" + z_min="$(echo "${z_coords}" | head -n 1)" + z_height_crystal="$(echo "scale=5; ${z_max} - ${z_min}" | bc)" + z_translate="$(echo "scale=5; ${z_height} + ${z_max}" | bc)" + z_height_2slab="$(echo "scale=5; ${z_height} + ${z_height_crystal} + ${z_buffer}" | bc)" + + # insert "-" at column 39 in all lines of gro file to reflect crystal on z-axis + awk '{print substr($0,1,38)"-"substr($0,40)}' "crystal.gro" >"crystal_reflected.gro" + head -n 2 crystal.gro >temp.txt + tail -n +3 crystal_reflected.gro >>temp.txt + head -n -1 temp.txt >temp2.txt + mv temp2.txt temp.txt + tail -n 1 crystal.gro >>temp.txt + mv temp.txt crystal_reflected.gro + + # move reflected crystal to top of box + "${GMX_BIN}" editconf \ + -f "crystal_reflected.gro" \ + -o "crystal_reflected.gro" \ + -translate 0 0 "${z_translate}" + + # get crystal coordinates for a dat file + z_cryst="$(awk 'NR>2 {print $6}' "crystal_reflected.gro")" + z_cryst="$(echo "${z_cryst}" | head -n -1)" + y_cryst="$(awk 'NR>2 {print $5}' "crystal_reflected.gro")" + y_cryst="$(echo "${y_cryst}" | head -n -1)" + x_cryst="$(awk 'NR>2 {print $4}' "crystal_reflected.gro")" + x_cryst="$(echo "${x_cryst}" | head -n -1)" + paste <(echo "${x_cryst}") <(echo "${y_cryst}") <(echo "${z_cryst}") >positions.dat + + # increase box size in z-dimension by z_height_crystal + cp -np "${sim_name}.gro" "${sim_name}_2slab_pre.gro" || exit 1 + sed -i "s/${z_height}/${z_height_2slab}/" "${sim_name}_2slab_pre.gro" + + # convert box and crystal to pdb files + "${GMX_BIN}" editconf \ + -f "${sim_name}_2slab_pre.gro" \ + -o "${sim_name}_2slab_pre.pdb" + sed -i '/^TER/d' "${sim_name}_2slab_pre.pdb" + sed -i '/^ENDMDL/d' "${sim_name}_2slab_pre.pdb" + "${GMX_BIN}" editconf \ + -f "crystal_reflected.gro" \ + -o "crystal_reflected.pdb" + sed -i "/^TITLE.*/d" "crystal_reflected.pdb" + sed -i "/^REMARK.*/d" "crystal_reflected.pdb" + sed -i "/^CRYST1.*/d" "crystal_reflected.pdb" + sed -i "/^MODEL.*/d" "crystal_reflected.pdb" + + # merge pdb files into gro file + \cat "${sim_name}_2slab_pre.pdb" "crystal_reflected.pdb" >"${sim_name}_2slab.pdb" + "${GMX_BIN}" editconf \ + -f "${sim_name}_2slab.pdb" \ + -o "${sim_name}_2slab.gro" + + # move files to archive directory + mkdir -p "${archive_dir}" + mv "crystal_reflected.gro" "${archive_dir}/" + mv "crystal_reflected.pdb" "${archive_dir}/" + mv "positions.dat" "${archive_dir}/" + mv "${sim_name}_2slab_pre.gro" "${archive_dir}/" + mv "${sim_name}_2slab_pre.pdb" "${archive_dir}/" + mv "${sim_name}_2slab.pdb" "${archive_dir}/" + cp "${sim_name}_2slab.gro" "${archive_dir}/" + } >>"${log_file}" 2>&1 +fi + +# TODO: make new topology files with 2slab + +# TODO: make new index file From 98b5ca8f70efad3442df16df0d6303bc5cbdbabd Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Tue, 5 Mar 2024 11:59:10 -0800 Subject: [PATCH 04/11] NPT equilibration and production no longer freeze crystal atoms --- .vscode/settings.json | 1 + .../mdp/molecular-dynamics/npt_eqbm.mdp | 2 +- .../mdp/molecular-dynamics/nvt_prod_100ns.mdp | 3 -- .../mdp/molecular-dynamics/nvt_prod_500ns.mdp | 3 -- scripts/method/equilibration.sh | 35 ++++++++----------- scripts/method/equilibration_hremd.sh | 2 +- scripts/method/initialization.sh | 17 ++++++++- scripts/method/sampling_hremd.sh | 2 +- scripts/method/sampling_md.sh | 2 +- scripts/method/sampling_metadynamics.sh | 2 +- scripts/method/sampling_opes_explore.sh | 2 +- scripts/method/sampling_opes_one.sh | 2 +- scripts/utilities/second_slab.sh | 6 ++++ ...A_0Ca_104calcite_2nm_crystal_5nm_height.sh | 2 +- ...A_0Ca_104calcite_5nm_crystal_6nm_height.sh | 2 +- ...2Ca_104calcite_12nm_crystal_12nm_height.sh | 2 +- ...A_0Ca_104calcite_2nm_crystal_3nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_3nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_4nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_3nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_4nm_height.sh | 2 +- ...A_0Ca_104calcite_2nm_crystal_4nm_height.sh | 2 +- ...0Ca_104calcite_12nm_crystal_13nm_height.sh | 2 +- ...2Ca_104calcite_12nm_crystal_13nm_height.sh | 2 +- ...A_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...A_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ...n_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ...c_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ...H_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ..._8Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...32Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...64Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../1.0_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...aCl2_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...aCO3_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16AA_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16An_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16Al_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16Ac_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../5-one-opes-params/1.0_lowbarrier3.sh | 2 +- .../5-one-opes-params/2.0_lowbarrier5.sh | 2 +- .../3.0_lowbarrier5_geom370.sh | 2 +- .../4.0_lowbarrier5_geom350.sh | 2 +- .../5.0_lowbarrier5_lower305_geom370.sh | 2 +- .../6.0_lowbarrier5_lower304_upper374.sh | 2 +- .../7.0_lowbarrier8_lower304_upper374.sh | 2 +- .../1.0_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.1_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.2_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.3_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.4_16paa_0Ca_9nmcrystal.sh | 2 +- .../2.0_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.1_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.2_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.3_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.4_16paan_0Ca_9nmcrystal.sh | 2 +- .../3.0_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.1_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.2_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.3_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.4_32paa_0Ca_12nmcrystal.sh | 2 +- .../4.0_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.1_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.2_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.3_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.4_32paan_0Ca_12nmcrystal.sh | 2 +- .../5.0_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.1_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.2_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.3_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.4_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../1.0_104calcite_9nm_crystal_10nm_height.sh | 8 ++--- ...aCl2_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16AA_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../4.0_16paa_0Ca_9nmcrystal.sh | 8 ++--- 84 files changed, 121 insertions(+), 112 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index ce2049a..4bd22e7 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -66,6 +66,7 @@ "Lenantiomer", "libplumed", "linewidth", + "linpot", "lowbarrier", "Makefiles", "mathtext", diff --git a/parameters/mdp/molecular-dynamics/npt_eqbm.mdp b/parameters/mdp/molecular-dynamics/npt_eqbm.mdp index 8871727..f57d190 100644 --- a/parameters/mdp/molecular-dynamics/npt_eqbm.mdp +++ b/parameters/mdp/molecular-dynamics/npt_eqbm.mdp @@ -5,7 +5,7 @@ ;;; Run control ;;; integrator = md ; "steep" for energy minimization and "md" for a leap frog algorithm for integrating Newton's eq of motion dt = 0.001 ; 1 femtosecond -nsteps = 5000000 ; 5 nanoseconds +nsteps = 500000 ; 1 nanosecond comm-mode = Linear ; "Linear" (remove center for mass translation) "Angular" ( >> >> and rotation around the center of mass) "None" (no restric) nstcomm = 100 ; [steps] frequency for center of mass motion removal comm-grps = Aqueous Crystal ; groups for which the center of mass motion is removed diff --git a/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp b/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp index 56965c4..171faf1 100644 --- a/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp +++ b/parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp @@ -50,9 +50,6 @@ constraint-algorithm = lincs ; chooses which solver satisfies any no lincs-order = 4 ; accuracy of lincs: the number of matrices in the expansion for the matrix inversion lincs-iter = 1 ; number of iterative corrections to matrix inversion to compensate for lengthening due to rotation lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle -;;; Frozen groups ;;; -freezegrps = Frozen ; groups that are to be frozen -freezedim = Y Y Y ; directions in which the groups are frozen ;;; Vacuum parameters ;;; nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential diff --git a/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp b/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp index 3ce9e76..d45d636 100644 --- a/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp +++ b/parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp @@ -50,9 +50,6 @@ constraint-algorithm = lincs ; chooses which solver satisfies any no lincs-order = 4 ; accuracy of lincs: the number of matrices in the expansion for the matrix inversion lincs-iter = 1 ; number of iterative corrections to matrix inversion to compensate for lengthening due to rotation lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle -;;; Frozen groups ;;; -freezegrps = Frozen ; groups that are to be frozen -freezedim = Y Y Y ; directions in which the groups are frozen ;;; Vacuum parameters ;;; nwall = 0 ; number of walls wall-type = 9-3 ; type of wall potential diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 8391f0b..c01303a 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -102,7 +102,8 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 + # FIXME: wall-atomtype is leading to instability, may need to be removed + # sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 fi @@ -187,8 +188,9 @@ else cp -np "${previous_archive_dir}/${previous_sim_name}.gro" "${previous_sim_name}.gro" || exit 1 cp "${mdp_file_npt}" "${sim_name}.mdp" || exit 1 - # freeze atoms in mdp file - sed -i 's/freezegrps.*/freezegrps = Crystal/g' "${sim_name}.mdp" || exit 1 + # delete lines from frozen groups + sed -i '/freezegrps/d' "${sim_name}.mdp" || exit 1 + sed -i '/freezedim/d' "${sim_name}.mdp" || exit 1 # replace temperature and pressure in mdp file sed -i 's/ref-t.*/ref-t = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 @@ -204,8 +206,9 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 - echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 + # FIXME: wall-atomtype is leading to instability, may need to be removed + # sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 + # echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 fi # make tpr file @@ -283,10 +286,12 @@ fi previous_sim_gro_last_line="$(tail -n 1 "${previous_archive_dir}/${previous_sim_name}.gro")" previous_sim_gro_box_dimensions="$(echo "${previous_sim_gro_last_line}" | awk '{print $1, $2, $3}')" echo "DEBUG: NVT system dimensions: ${previous_sim_gro_box_dimensions}" + # get last line of current sim gro file sim_gro_last_line="$(tail -n 1 "${archive_dir}/${sim_name}.gro")" sim_gro_box_dimensions="$(echo "${sim_gro_last_line}" | awk '{print $1, $2, $3}')" echo "DEBUG: NPT system dimensions: ${sim_gro_box_dimensions}" + # calculate percent change in each dimension # shellcheck disable=SC2206 previous_sim_gro_box_dimensions_array=(${previous_sim_gro_box_dimensions}) @@ -309,21 +314,6 @@ if [[ "${N_SLAB}" -eq 2 ]]; then rm "${sim_name}.gro" fi -# ####################################################################################### -# Make box orthorhombic ############################################################## -# ####################################################################################### -echo "INFO: Making box orthorhombic" -{ - cp -np "${archive_dir}/${sim_name}.gro" "${archive_dir}/${sim_name}_triclinic.gro" - "${GMX_BIN}" trjconv \ - -f "${archive_dir}/${sim_name}.gro" \ - -s "${archive_dir}/${sim_name}.tpr" \ - -o "${archive_dir}/${sim_name}.gro" \ - -ur 'rect' <>"${log_file}" 2>&1 - # ####################################################################################### # Production equilibration ############################################################## # ####################################################################################### @@ -345,6 +335,9 @@ else # copy output files from NVT equilibration cp -np "${previous_archive_dir}/${previous_sim_name}.gro" "${previous_sim_name}.gro" || exit 1 + # delete lines from frozen groups + sed -i '/freezegrps/d' "${sim_name}.mdp" || exit 1 + sed -i '/freezedim/d' "${sim_name}.mdp" || exit 1 # replace temperature and pressure in mdp file cp "${mdp_file_prod}" "${sim_name}.mdp" || exit 1 sed -i 's/ref-t.*/ref-t = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 @@ -361,7 +354,7 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/method/equilibration_hremd.sh b/scripts/method/equilibration_hremd.sh index bc3c87a..608d799 100755 --- a/scripts/method/equilibration_hremd.sh +++ b/scripts/method/equilibration_hremd.sh @@ -139,7 +139,7 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/method/initialization.sh b/scripts/method/initialization.sh index 37ac99a..c5b3a6e 100755 --- a/scripts/method/initialization.sh +++ b/scripts/method/initialization.sh @@ -111,7 +111,8 @@ echo "INFO: Copying input files to working directory" sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "mdin.mdp" sed -i 's/^pbc .*/pbc = xy/g' "mdin.mdp" sed -i 's/^nwall .*/nwall = 2/g' "mdin.mdp" - sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "mdin.mdp" + # FIXME: this is not working + # sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "mdin.mdp" fi } >>"${log_file}" 2>&1 @@ -403,6 +404,20 @@ echo "INFO: Adding positional restraints" fi } >>"${log_file}" 2>&1 +# ####################################################################################### +# Make box orthorhombic ############################################################## +# ####################################################################################### +echo "INFO: Making box orthorhombic" +{ + "${GMX_BIN}" trjconv \ + -f "${sim_name}.gro" \ + -s "${sim_name}.tpr" \ + -o "${sim_name}.gro" \ + -ur 'rect' <>"${log_file}" 2>&1 + # ############################################################################## # Create Topology ############################################################## # ############################################################################## diff --git a/scripts/method/sampling_hremd.sh b/scripts/method/sampling_hremd.sh index 9e0bc31..6a6b4d8 100755 --- a/scripts/method/sampling_hremd.sh +++ b/scripts/method/sampling_hremd.sh @@ -126,7 +126,7 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/method/sampling_md.sh b/scripts/method/sampling_md.sh index 032e41f..ce2a3cd 100755 --- a/scripts/method/sampling_md.sh +++ b/scripts/method/sampling_md.sh @@ -107,7 +107,7 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/method/sampling_metadynamics.sh b/scripts/method/sampling_metadynamics.sh index a227e3e..1b35a64 100755 --- a/scripts/method/sampling_metadynamics.sh +++ b/scripts/method/sampling_metadynamics.sh @@ -100,7 +100,7 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/method/sampling_opes_explore.sh b/scripts/method/sampling_opes_explore.sh index 3c2dcb7..310824a 100755 --- a/scripts/method/sampling_opes_explore.sh +++ b/scripts/method/sampling_opes_explore.sh @@ -94,7 +94,7 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/method/sampling_opes_one.sh b/scripts/method/sampling_opes_one.sh index 9050909..893b3b6 100755 --- a/scripts/method/sampling_opes_one.sh +++ b/scripts/method/sampling_opes_one.sh @@ -110,7 +110,7 @@ sim_name="prod_opes_one_multicv" sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - if [[ "${N_SLABS}" -eq 2 ]]; then + if [[ "${N_SLAB}" -eq 2 ]]; then sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WR WR/g' "${sim_name}.mdp" || exit 1 fi fi diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index 0455d2a..54e6069 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -98,6 +98,12 @@ else } >>"${log_file}" 2>&1 fi +# ############################################################################## +# Remake system topology ####################################################### +# ############################################################################## # TODO: make new topology files with 2slab +# ############################################################################## +# Remake system index ########################################################## +# ############################################################################## # TODO: make new index file diff --git a/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh b/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh index 116fede..f1bebd9 100755 --- a/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh +++ b/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh b/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh index d8cef03..4cb59c4 100755 --- a/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh +++ b/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='8' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh b/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh index a1de02e..462a62a 100755 --- a/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh +++ b/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh index 2e170de..692abe5 100755 --- a/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='3' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh index c02bb34..13cc1a3 100755 --- a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='3' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh index 176777b..8a7f98e 100755 --- a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='3' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh index cdc3202..1a73c42 100755 --- a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='4' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh index bbb02e1..33a2101 100755 --- a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='4' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh index 86ab381..6e6c5e9 100755 --- a/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='0.14' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='0.99' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='4' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh b/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh index 86ebc43..5f9ebca 100755 --- a/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh +++ b/submission/input/1-model-system/1_32PAA_0Ca_104calcite_12nm_crystal_13nm_height.sh @@ -25,7 +25,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh b/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh index c73c5e6..cf7248f 100755 --- a/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh +++ b/submission/input/1-model-system/2_32PAA_32Ca_104calcite_12nm_crystal_13nm_height.sh @@ -25,7 +25,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh index d8a0321..0343532 100755 --- a/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/1-model-system/3_8PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -25,7 +25,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='8' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 85002ed..54b1774 100755 --- a/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 2ccabf0..3bcf1bd 100755 --- a/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 1b11f94..68d29cd 100755 --- a/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index d6481d3..522a92d 100755 --- a/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index fccf2ff..c780906 100755 --- a/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh index 01df74a..05c4826 100755 --- a/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh index 6e26ba2..7941f8c 100755 --- a/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh index ebb39e7..f015f99 100755 --- a/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh index 6f0b868..4e791e3 100755 --- a/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh index 2dd166e..7264711 100755 --- a/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh index 658a70e..0ca3f21 100755 --- a/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh index 1c153b9..47136ee 100755 --- a/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='2.8' # z-coordinate of bottom of bulk part of crystal in n export PDB_BULK_ZMAX='3.2' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh index 1b57a09..7177fd7 100755 --- a/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh index 50b7873..ec008a0 100755 --- a/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh index b15192e..16516ab 100755 --- a/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh index 1524266..fee3687 100755 --- a/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 3f6f190..1ad78fa 100755 --- a/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index 7ed9b31..bcfc31f 100755 --- a/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh index b11c92d..a32d4a7 100755 --- a/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='64' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh index da6f622..fdf6fe5 100755 --- a/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh index 678f01b..a3a5561 100755 --- a/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh index 0fc8db9..2176aa4 100755 --- a/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh index dd8c6be..7911128 100755 --- a/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/1.0_lowbarrier3.sh b/submission/input/5-one-opes-params/1.0_lowbarrier3.sh index 58eeb8b..cfce1f0 100755 --- a/submission/input/5-one-opes-params/1.0_lowbarrier3.sh +++ b/submission/input/5-one-opes-params/1.0_lowbarrier3.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/2.0_lowbarrier5.sh b/submission/input/5-one-opes-params/2.0_lowbarrier5.sh index 682be25..ef1c88a 100755 --- a/submission/input/5-one-opes-params/2.0_lowbarrier5.sh +++ b/submission/input/5-one-opes-params/2.0_lowbarrier5.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh b/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh index 5c0606f..ccc88c0 100755 --- a/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh +++ b/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh b/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh index 2487df5..05480ea 100755 --- a/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh +++ b/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh b/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh index e31bc6c..3e4ab99 100755 --- a/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh +++ b/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh b/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh index cbe7649..c2b6a42 100755 --- a/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh +++ b/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh b/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh index 697cc9f..af8b754 100755 --- a/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh +++ b/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh @@ -39,7 +39,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh index 9005c04..44b3c59 100755 --- a/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh index 1486864..e61fbc3 100755 --- a/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh index a480ded..fca41ff 100755 --- a/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh index 46d9cfd..9f48e03 100755 --- a/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh index ad0e445..f0054b9 100755 --- a/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh index a6808c2..d1c4fe3 100755 --- a/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh index 7cf0446..c5df8f9 100755 --- a/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh index b6c1717..8b1ea67 100755 --- a/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh index 2c2d069..1e96436 100755 --- a/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh index fa71f1f..7830e7e 100755 --- a/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh index 47e7ed2..8d136c2 100755 --- a/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh index 1ab91ee..097267f 100755 --- a/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh index ca080e2..0b08f86 100755 --- a/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh index 1573020..5a2088c 100755 --- a/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh index 25126e7..7df99ee 100755 --- a/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh index d90153e..e6f514f 100755 --- a/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh index a8498f4..7100c85 100755 --- a/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh index 7fb323b..3738ec1 100755 --- a/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh index 23f3831..c569133 100755 --- a/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh index 4a65168..7494ef4 100755 --- a/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh index 868bd20..a1baf8a 100755 --- a/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh index ef73588..ea64052 100755 --- a/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh index 2f97c34..0074c07 100755 --- a/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh index a0b84ae..00981ab 100755 --- a/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh index 015ea6d..1edab6c 100755 --- a/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='6.52' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='6.83' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='32' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 55cbc64..75299e0 100755 --- a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -8,9 +8,9 @@ # Hardware #################################################################### -export CPU_THREADS='-1' # number of CPU threads to use (-1 = all available) -export PIN_OFFSET='-1' # offset for CPU thread pinning (-1 = no offset) -export GPU_IDS='-1' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) +export CPU_THREADS='4' # number of CPU threads to use (-1 = all available) +export PIN_OFFSET='0' # offset for CPU thread pinning (-1 = no offset) +export GPU_IDS='0' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) # System components ########################################################### @@ -41,7 +41,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index 8d48068..ce30697 100755 --- a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh index a212a0c..ee392e6 100755 --- a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh index 36cedfa..e171e0b 100755 --- a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh @@ -8,9 +8,9 @@ # Hardware #################################################################### -export CPU_THREADS='-1' # number of CPU threads to use (-1 = all available) -export PIN_OFFSET='-1' # offset for CPU thread pinning (-1 = no offset) -export GPU_IDS='-1' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) +export CPU_THREADS='4' # number of CPU threads to use (-1 = all available) +export PIN_OFFSET='4' # offset for CPU thread pinning (-1 = no offset) +export GPU_IDS='2' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) # System components ########################################################### @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLABS='1' # number of crystal slabs {1, 2} +export N_SLAB='1' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions From a7bb9ace72514f3f4450a5027ce0ded5cb53b88c Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Tue, 5 Mar 2024 13:53:35 -0800 Subject: [PATCH 05/11] Add TwoSlabTopGenerator class to generate topology for a system with two slabs --- python/second_slab_topology.py | 57 +++++++++++++++++++ scripts/method/equilibration.sh | 10 +++- scripts/utilities/second_slab.sh | 8 ++- .../1.0_104calcite_9nm_crystal_10nm_height.sh | 2 +- 4 files changed, 70 insertions(+), 7 deletions(-) create mode 100644 python/second_slab_topology.py diff --git a/python/second_slab_topology.py b/python/second_slab_topology.py new file mode 100644 index 0000000..41f71fb --- /dev/null +++ b/python/second_slab_topology.py @@ -0,0 +1,57 @@ +from pathlib import Path + + +class TwoSlabTopGenerator: + + def __init__(self, input_top: Path, verbose: bool = False) -> None: + self.input_top = Path(input_top) + with open(self.input_top, "r", encoding="utf-8") as f: + self.top = f.read() + + # split top into dictionary of sections. Sections are separated by [section_name] + self.sections = {} + section_name = None + for line in self.top.split("\n"): + if line.startswith("["): + section_name = line + self.sections[section_name] = [] + else: + self.sections[section_name].append(line) + if verbose: + print(f"Parsed sections: {self.sections.keys()}") + + self.generated_top = False + + # TODO: calculate the number of atoms in the system + # TODO: calculate number of atoms in original slab + + def generate(self, output_top: Path) -> None: + self._add_atoms() + self._add_bonds() + self._add_angles() + self._add_dihedrals() + self._add_position_restraints() + + self.generated_top = True + self.save(output_top) + + def _add_atoms(self) -> None: + pass + + def _add_bonds(self) -> None: + pass + + def _add_angles(self) -> None: + pass + + def _add_dihedrals(self) -> None: + pass + + def _add_position_restraints(self) -> None: + pass + + def save(self, output_top: Path) -> None: + if not self.generated_top: + raise ValueError("Topology has not been generated yet") + with open(output_top, "w", encoding="utf-8") as f: + f.write(self.top) diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index c01303a..775b04f 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -319,10 +319,15 @@ fi # ####################################################################################### echo "INFO: Starting production equilibration" previous_sim_name="${sim_name}" -previous_archive_dir="${archive_dir}" sim_name="prod_eqbm" archive_dir="3-pre-production" +if [[ "${N_SLAB}" -eq 2 ]]; then + previous_archive_dir="3-second-slab" +else + previous_archive_dir="${archive_dir}" +fi + # check if output gro file already exists if [[ -f "${archive_dir}/${sim_name}.gro" ]]; then echo "WARNING: ${archive_dir}/${sim_name}.gro already exists" @@ -332,14 +337,13 @@ else # if tpr file does not exist, create it if [[ ! -f "${sim_name}.tpr" ]]; then echo "DEBUG: Creating tpr file" - # copy output files from NVT equilibration cp -np "${previous_archive_dir}/${previous_sim_name}.gro" "${previous_sim_name}.gro" || exit 1 + cp "${mdp_file_prod}" "${sim_name}.mdp" || exit 1 # delete lines from frozen groups sed -i '/freezegrps/d' "${sim_name}.mdp" || exit 1 sed -i '/freezedim/d' "${sim_name}.mdp" || exit 1 # replace temperature and pressure in mdp file - cp "${mdp_file_prod}" "${sim_name}.mdp" || exit 1 sed -i 's/ref-t.*/ref-t = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/gen-temp.*/gen-temp = '"${TEMPERATURE_K}/g" "${sim_name}.mdp" || exit 1 sed -i 's/ref-p.*/ref-p = '"${PRESSURE_BAR} ${PRESSURE_BAR}/g" "${sim_name}.mdp" || exit 1 diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index 54e6069..67b2483 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -9,7 +9,7 @@ # submission/input/*.sh script. Script should only be called from # the equilibration.sh script. -z_buffer="0.1" # [nm] +z_buffer="0.0" # [nm] sim_name="npt_eqbm" archive_dir="3-second-slab" log_file="second_slab.log" @@ -18,7 +18,7 @@ log_file="second_slab.log" # Add second slab to box ####################################################### # ############################################################################## # check if output gro file already exists -if [[ -f "${sim_name}_2slab.gro" ]]; then +if [[ -f "${archive_dir}/${sim_name}_2slab.gro" ]]; then echo "DEBUG: Second slab already added" else { @@ -88,13 +88,15 @@ else # move files to archive directory mkdir -p "${archive_dir}" + mv "crystal.gro" "${archive_dir}/" mv "crystal_reflected.gro" "${archive_dir}/" mv "crystal_reflected.pdb" "${archive_dir}/" mv "positions.dat" "${archive_dir}/" mv "${sim_name}_2slab_pre.gro" "${archive_dir}/" mv "${sim_name}_2slab_pre.pdb" "${archive_dir}/" mv "${sim_name}_2slab.pdb" "${archive_dir}/" - cp "${sim_name}_2slab.gro" "${archive_dir}/" + mv "${sim_name}_2slab.gro" "${archive_dir}/" + cp "${archive_dir}/${sim_name}_2slab.gro" "${archive_dir}/${sim_name}.gro" } >>"${log_file}" 2>&1 fi diff --git a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 75299e0..e6fb3f6 100755 --- a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -41,7 +41,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLAB='1' # number of crystal slabs {1, 2} +export N_SLAB='2' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions From 112071e84652aa32eb63e421cc36d2a081666976 Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Tue, 5 Mar 2024 17:09:20 -0800 Subject: [PATCH 06/11] WIP: need to adjust index making. Coordinates and topology stable --- python/second_slab_topology.py | 57 -------------------- python/twoslab_index.py | 92 ++++++++++++++++++++++++++++++++ scripts/utilities/second_slab.sh | 63 ++++++++++++++++++---- 3 files changed, 146 insertions(+), 66 deletions(-) delete mode 100644 python/second_slab_topology.py create mode 100644 python/twoslab_index.py diff --git a/python/second_slab_topology.py b/python/second_slab_topology.py deleted file mode 100644 index 41f71fb..0000000 --- a/python/second_slab_topology.py +++ /dev/null @@ -1,57 +0,0 @@ -from pathlib import Path - - -class TwoSlabTopGenerator: - - def __init__(self, input_top: Path, verbose: bool = False) -> None: - self.input_top = Path(input_top) - with open(self.input_top, "r", encoding="utf-8") as f: - self.top = f.read() - - # split top into dictionary of sections. Sections are separated by [section_name] - self.sections = {} - section_name = None - for line in self.top.split("\n"): - if line.startswith("["): - section_name = line - self.sections[section_name] = [] - else: - self.sections[section_name].append(line) - if verbose: - print(f"Parsed sections: {self.sections.keys()}") - - self.generated_top = False - - # TODO: calculate the number of atoms in the system - # TODO: calculate number of atoms in original slab - - def generate(self, output_top: Path) -> None: - self._add_atoms() - self._add_bonds() - self._add_angles() - self._add_dihedrals() - self._add_position_restraints() - - self.generated_top = True - self.save(output_top) - - def _add_atoms(self) -> None: - pass - - def _add_bonds(self) -> None: - pass - - def _add_angles(self) -> None: - pass - - def _add_dihedrals(self) -> None: - pass - - def _add_position_restraints(self) -> None: - pass - - def save(self, output_top: Path) -> None: - if not self.generated_top: - raise ValueError("Topology has not been generated yet") - with open(output_top, "w", encoding="utf-8") as f: - f.write(self.top) diff --git a/python/twoslab_index.py b/python/twoslab_index.py new file mode 100644 index 0000000..b9db40f --- /dev/null +++ b/python/twoslab_index.py @@ -0,0 +1,92 @@ +# standard library +from argparse import ArgumentParser +from pathlib import Path + +# third-party +import numpy as np +import gromacs as gmx + + +class TwoSlabIdxGenerator: + + def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = False) -> None: + # parse input index file + self.ndx = gmx.fileformats.ndx.NDX() + self.ndx.read(input_idx) + + # parse input gro file + self.input_gro = Path(input_gro) + with open(self.input_gro, "r", encoding="utf-8") as f: + self.gro = f.read() + self.n_atoms = int(self.gro.split("\n")[1]) + n_crb_atoms = len([line for line in self.gro.split("\n") if "CRB" in line]) + self.n_crystal_atoms = int(3 * n_crb_atoms / 2) + + if verbose: + print(f"Number of atoms: {self.n_atoms}") + print(f"Number of crystal atoms in first slab: {self.n_crystal_atoms}") + print(f"Index groups: {self.ndx.keys()}") + + def _update_original_index(self, min_index: int, offset: int) -> None: + # update original index for all groups with offset from second slab + for group in self.ndx.keys(): + self.ndx[group] = [ + i + offset if i >= min_index else i for i in self.ndx[group] + ] + + def _add_second_slab(self, min_index: int, n_atoms: int) -> None: + # get atoms in frozen and mobile groups + frozen = self.ndx["Frozen"] + frozen_slab = frozen[frozen < min_index] + mobile = self.ndx["Mobile"] + mobile_slab = mobile[mobile < min_index] + + # TODO: add relevant atoms to frozen and mobile groups + frozen_second_slab = [i + min_index for i in frozen_slab] + mobile_second_slab = [i + min_index for i in mobile_slab] + self.ndx["Frozen"] = np.append(frozen, frozen_second_slab) + self.ndx["Mobile"] = np.append(mobile, mobile_second_slab) + + # FIXME: for all subgroups of "Crystal", only add relevant atoms + # add second slab to all groups matching patterns + patterns = ["Crystal", "System", "non-Water"] + group_new = np.array([min_index + i for i in range(1, n_atoms + 1)]) + for group in self.ndx.items(): + group = group[0] + if any(pattern in group for pattern in patterns): + group_original = self.ndx[group] + self.ndx[group] = np.append(group_original, group_new) + + def generate(self, output_top: Path) -> None: + self._update_original_index(self.n_crystal_atoms, self.n_crystal_atoms) + self._add_second_slab(self.n_crystal_atoms, self.n_crystal_atoms) + self.save(output_top) + + def save(self, output_top: Path) -> None: + self.ndx.write(output_top) + + +def main(): + parser = ArgumentParser( + description="Generate a topology file for a system with two slabs" + ) + parser.add_argument( + "-i", "--input-idx", type=Path, required=True, help="Input index file" + ) + parser.add_argument( + "-g", "--input-gro", type=Path, required=True, help="Input coordinate file" + ) + parser.add_argument( + "-o", "--output-idx", type=Path, required=True, help="Output index file" + ) + parser.add_argument( + "-v", "--verbose", action="store_true", help="Print extra information" + ) + args = parser.parse_args() + + generator = TwoSlabIdxGenerator(args.input_idx, args.input_gro, args.verbose) + generator.generate(args.output_idx) + + +if __name__ == "__main__": + main() diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index 67b2483..e0d20b5 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -14,6 +14,10 @@ sim_name="npt_eqbm" archive_dir="3-second-slab" log_file="second_slab.log" +# find path to this script +script_path="$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd)" +project_path="${script_path}/../.." + # ############################################################################## # Add second slab to box ####################################################### # ############################################################################## @@ -22,6 +26,8 @@ if [[ -f "${archive_dir}/${sim_name}_2slab.gro" ]]; then echo "DEBUG: Second slab already added" else { + echo "DEBUG: Adding second slab to box" + # copy crystal.pdb from initialization cp -np "../1-energy-minimization/crystal.gro" "crystal.gro" || exit 1 @@ -70,18 +76,20 @@ else "${GMX_BIN}" editconf \ -f "${sim_name}_2slab_pre.gro" \ -o "${sim_name}_2slab_pre.pdb" - sed -i '/^TER/d' "${sim_name}_2slab_pre.pdb" - sed -i '/^ENDMDL/d' "${sim_name}_2slab_pre.pdb" "${GMX_BIN}" editconf \ -f "crystal_reflected.gro" \ -o "crystal_reflected.pdb" - sed -i "/^TITLE.*/d" "crystal_reflected.pdb" - sed -i "/^REMARK.*/d" "crystal_reflected.pdb" - sed -i "/^CRYST1.*/d" "crystal_reflected.pdb" - sed -i "/^MODEL.*/d" "crystal_reflected.pdb" + + # remove unnecessary lines from pdb files + sed -i '/^TER/d' "crystal_reflected.pdb" + sed -i '/^ENDMDL/d' "crystal_reflected.pdb" + sed -i "/^TITLE.*/d" "${sim_name}_2slab_pre.pdb + sed -i "/^REMARK.*/d" "${sim_name}_2slab_pre.pdb + sed -i "/^CRYST1.*/d" "${sim_name}_2slab_pre.pdb + sed -i "/^MODEL.*/d" "${sim_name}_2slab_pre.pdb # merge pdb files into gro file - \cat "${sim_name}_2slab_pre.pdb" "crystal_reflected.pdb" >"${sim_name}_2slab.pdb" + \cat "crystal_reflected.pdb" "${sim_name}_2slab_pre.pdb" >"${sim_name}_2slab.pdb" "${GMX_BIN}" editconf \ -f "${sim_name}_2slab.pdb" \ -o "${sim_name}_2slab.gro" @@ -103,9 +111,46 @@ fi # ############################################################################## # Remake system topology ####################################################### # ############################################################################## -# TODO: make new topology files with 2slab + +# update number of atoms in topology file +if [[ -f "${archive_dir}/topol.top" ]]; then + echo "DEBUG: Topology file already updated" + +else + echo "DEBUG: Updating topology file" + { + # get all lines [ molecules ] and following from topol.top + grep -A 1000 "molecules" topol.top >temp.txt + n_mol_slab="$(grep "Ion_chain_X" temp.txt | awk '{print $2}')" + n_mol_2slab="$(echo "2 * ${n_mol_slab}" | bc)" + sed -i "s/${n_mol_slab}/${n_mol_2slab}/" temp.txt + # replace [ molecules ] and following in topol.top + sed -i '/molecules/,$d' topol.top + cat temp.txt >>topol.top + rm temp.txt + cp topol.top "${archive_dir}/" + } >>"${log_file}" 2>&1 + echo "DEBUG: n_mol_slab = ${n_mol_slab}" + echo "DEBUG: n_mol_2slab = ${n_mol_2slab}" + +fi # ############################################################################## # Remake system index ########################################################## # ############################################################################## -# TODO: make new index file + +# Current groups: + +if [[ -f "${archive_dir}/index.ndx" ]]; then + echo "DEBUG: Index file already updated" +else + # call python script to update index file + echo "DEBUG: Updating index file" + cp -np "index.ndx" "${archive_dir}/index_1slab.ndx" || exit 1 + python3 "${project_path}/python/twoslab_index.py" \ + -i "index.ndx" \ + -g "${sim_name}.gro" \ + -o "index.ndx" \ + -v || exit 1 + cp "index.ndx" "${archive_dir}/" +fi From e556f587d65c719ed964c05f3069d34779fe3372 Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Tue, 5 Mar 2024 21:07:30 -0800 Subject: [PATCH 07/11] WIP: appears 2-slab system is stable, but requires further testing --- .vscode/settings.json | 4 ++ python/twoslab_index.py | 87 +++++++++++++++++++++----------- scripts/method/equilibration.sh | 1 + scripts/utilities/second_slab.sh | 15 ++++++ 4 files changed, 77 insertions(+), 30 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 4bd22e7..8cc3b77 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -26,6 +26,7 @@ "downsample", "downsampled", "DREGRESSIONTEST", + "dtype", "eccrpa", "editconf", "ENDMDL", @@ -33,8 +34,10 @@ "eqbm", "ewald", "FFTW", + "fileformats", "fontsize", "forcefield", + "freezedim", "freezegrps", "Gaussians", "genion", @@ -150,6 +153,7 @@ "trjcat", "trjconv", "tunbiased", + "twoslab", "ungroup", "vaterite", "vdwradii", diff --git a/python/twoslab_index.py b/python/twoslab_index.py index b9db40f..a2dc69f 100644 --- a/python/twoslab_index.py +++ b/python/twoslab_index.py @@ -9,7 +9,7 @@ class TwoSlabIdxGenerator: - def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = False) -> None: + def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = True) -> None: # parse input index file self.ndx = gmx.fileformats.ndx.NDX() self.ndx.read(input_idx) @@ -19,9 +19,17 @@ def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = False) -> N with open(self.input_gro, "r", encoding="utf-8") as f: self.gro = f.read() self.n_atoms = int(self.gro.split("\n")[1]) - n_crb_atoms = len([line for line in self.gro.split("\n") if "CRB" in line]) - self.n_crystal_atoms = int(3 * n_crb_atoms / 2) + self.n_crystal_atoms = len(self.ndx["Crystal"]) + # input validation + total_atoms = self.n_atoms + if total_atoms != len(self.ndx["System"]): + raise ValueError( + "Number of atoms mismatch in System group:" + + f" {total_atoms} != {len(self.ndx['System'])}" + ) + + self.verbose = verbose if verbose: print(f"Number of atoms: {self.n_atoms}") print(f"Number of crystal atoms in first slab: {self.n_crystal_atoms}") @@ -29,37 +37,56 @@ def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = False) -> N def _update_original_index(self, min_index: int, offset: int) -> None: # update original index for all groups with offset from second slab - for group in self.ndx.keys(): - self.ndx[group] = [ - i + offset if i >= min_index else i for i in self.ndx[group] - ] - - def _add_second_slab(self, min_index: int, n_atoms: int) -> None: - # get atoms in frozen and mobile groups - frozen = self.ndx["Frozen"] - frozen_slab = frozen[frozen < min_index] - mobile = self.ndx["Mobile"] - mobile_slab = mobile[mobile < min_index] - - # TODO: add relevant atoms to frozen and mobile groups - frozen_second_slab = [i + min_index for i in frozen_slab] - mobile_second_slab = [i + min_index for i in mobile_slab] - self.ndx["Frozen"] = np.append(frozen, frozen_second_slab) - self.ndx["Mobile"] = np.append(mobile, mobile_second_slab) - - # FIXME: for all subgroups of "Crystal", only add relevant atoms + for key, value in self.ndx.items(): + updated = [i + offset if i > min_index else i for i in value] + self.ndx[key] = np.array(updated, dtype=int) + if self.verbose: + n_changed = sum([i > min_index for i in value]) + if n_changed > 0: + print(f"Updated {n_changed} indices in group {key}") + else: + print(f"No indices updated in group {key}") + + total_atoms = self.n_atoms + if total_atoms != len(self.ndx["System"]): + raise ValueError( + f"Number of atoms mismatch in System group: {total_atoms} != {len(self.ndx['System'])}" + ) + + def _add_second_slab(self, min_index: int) -> None: # add second slab to all groups matching patterns - patterns = ["Crystal", "System", "non-Water"] - group_new = np.array([min_index + i for i in range(1, n_atoms + 1)]) - for group in self.ndx.items(): - group = group[0] - if any(pattern in group for pattern in patterns): - group_original = self.ndx[group] - self.ndx[group] = np.append(group_original, group_new) + patterns = ["System", "non-Water", "Frozen", "Mobile", "Crystal"] + for key, value in self.ndx.items(): + if any(p in key for p in patterns): + group_new = np.array( + [i + min_index for i in value if i <= min_index], dtype=int + ) + if len(group_new) > 0: + self.ndx[key] = np.append(value, group_new, axis=0) + if self.verbose and len(group_new) > 0: + print(f"Added {len(group_new)} atoms to group {key}") + elif self.verbose: + print(f"No atoms added to group {key}") + + total_atoms = self.n_atoms + self.n_crystal_atoms + if total_atoms != len(self.ndx["System"]): + raise ValueError( + f"Number of atoms mismatch in System group: {total_atoms} != {len(self.ndx['System'])}" + ) + + def _sort(self) -> None: + for key, value in self.ndx.items(): + self.ndx[key] = np.sort(value) def generate(self, output_top: Path) -> None: self._update_original_index(self.n_crystal_atoms, self.n_crystal_atoms) - self._add_second_slab(self.n_crystal_atoms, self.n_crystal_atoms) + self._add_second_slab(self.n_crystal_atoms) + self._sort() + + assert self.n_atoms + self.n_crystal_atoms == max( + self.ndx["System"] + ), f"Number of atoms mismatch in System group: {self.n_atoms} != {max(self.ndx['System'])}" + self.save(output_top) def save(self, output_top: Path) -> None: diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 775b04f..35b0a04 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -327,6 +327,7 @@ if [[ "${N_SLAB}" -eq 2 ]]; then else previous_archive_dir="${archive_dir}" fi +echo "DEBUG: Using previous archive directory: ${previous_archive_dir}" # check if output gro file already exists if [[ -f "${archive_dir}/${sim_name}.gro" ]]; then diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index e0d20b5..e676365 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -147,10 +147,25 @@ else # call python script to update index file echo "DEBUG: Updating index file" cp -np "index.ndx" "${archive_dir}/index_1slab.ndx" || exit 1 + "${GMX_BIN}" make_ndx \ + -f "${sim_name}.gro" \ + -n "index.ndx" \ + -o "index.ndx" < Date: Tue, 5 Mar 2024 21:16:15 -0800 Subject: [PATCH 08/11] all simulations in 7 with 2 slabs --- .../2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../3.0_16AA_104calcite_9nm_crystal_10nm_height.sh | 2 +- submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index ce30697..93bc162 100755 --- a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLAB='1' # number of crystal slabs {1, 2} +export N_SLAB='2' # number of crystal slabs {1, 2} export N_MONOMER='0' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='0' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh index ee392e6..7c1036f 100755 --- a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLAB='1' # number of crystal slabs {1, 2} +export N_SLAB='2' # number of crystal slabs {1, 2} export N_MONOMER='1' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='16' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions diff --git a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh index e171e0b..e30becb 100755 --- a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh @@ -42,7 +42,7 @@ export PDB_BULK_ZMIN='4.62' # z-coordinate of bottom of bulk part of crystal in export PDB_BULK_ZMAX='5.09' # z-coordinate of top of bulk part of crystal in nm in PDB file # number of each component -export N_SLAB='1' # number of crystal slabs {1, 2} +export N_SLAB='2' # number of crystal slabs {1, 2} export N_MONOMER='16' # number of monomers in chain {1, 2, 5, 8, 16, 32} export N_CHAIN='1' # number of chains export N_CARBONATE='0' # number of aqueous carbonate ions From 5d5802474c2bc87db33b49c2401c3c5e827b5056 Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Wed, 6 Mar 2024 08:04:01 -0800 Subject: [PATCH 09/11] added docs to twoslab_index.py and small bug fixes to scripts --- python/twoslab_index.py | 140 ++++++++++++++++++++++++++++--- scripts/method/equilibration.sh | 5 -- scripts/method/initialization.sh | 2 - scripts/utilities/second_slab.sh | 45 ++++------ 4 files changed, 145 insertions(+), 47 deletions(-) diff --git a/python/twoslab_index.py b/python/twoslab_index.py index a2dc69f..7ee1f94 100644 --- a/python/twoslab_index.py +++ b/python/twoslab_index.py @@ -1,3 +1,37 @@ +""" +This module provides a class for generating index files for a system with +two slabs. + +The TwoSlabIdxGenerator class takes an input index file and an input gro file +as arguments and generates an index file for a system with two slabs. It +provides methods for updating the original index, adding the second slab to +groups matching patterns, sorting the indices, and saving the index file. + +Example usage: + generator = TwoSlabIdxGenerator(input_idx, input_gro) + generator.generate(output_idx) + +Attributes: + input_idx (Path): The path to the input index file. + input_gro (Path): The path to the input gro file. + verbose (bool): Whether to print verbose output. + +Methods: + __init__(input_idx: Path, input_gro: Path, verbose: bool = True): + Initializes the TwoSlabIdxGenerator object. + __repr__(): Returns a string representation of the TwoSlabIdxGenerator + object. + print(): Prints the index groups and the number of atoms in each group. + _update_original_index(min_index: int, offset: int): Updates the original + index for all groups with an offset from the second slab. + _add_second_slab(min_index: int): Adds the second slab to all groups + matching patterns. + _sort(): Sorts the indices in each group. + generate(output_top: Path): Generates the index file for the system with + two slabs. + save(output_top: Path): Saves the index file to the specified path. +""" + # standard library from argparse import ArgumentParser from pathlib import Path @@ -8,6 +42,34 @@ class TwoSlabIdxGenerator: + """ + A class for generating index files for a system with two slabs. + + Args: + input_idx (Path): The path to the input index file. + input_gro (Path): The path to the input gro file. + verbose (bool, optional): Whether to print verbose output. Defaults to True. + + Attributes: + ndx (gmx.fileformats.ndx.NDX): The parsed input index file. + input_gro (Path): The path to the input gro file. + gro (str): The content of the input gro file. + n_atoms (int): The total number of atoms in the system. + n_crystal_atoms (int): The number of crystal atoms in the first slab. + verbose (bool): Whether to print verbose output. + + Methods: + __repr__(): Returns a string representation of the TwoSlabIdxGenerator object. + print(): Prints the index groups and the number of atoms in each group. + _update_original_index(min_index: int, offset: int): Updates the + original index for all groups with an offset from the second slab. + _add_second_slab(min_index: int): Adds the second slab to all groups + matching patterns. + _sort(): Sorts the indices in each group. + generate(output_top: Path): Generates the index file for the system + with two slabs. + save(output_top: Path): Saves the index file to the specified path. + """ def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = True) -> None: # parse input index file @@ -35,8 +97,35 @@ def __init__(self, input_idx: Path, input_gro: Path, verbose: bool = True) -> No print(f"Number of crystal atoms in first slab: {self.n_crystal_atoms}") print(f"Index groups: {self.ndx.keys()}") + def __repr__(self) -> str: + return ( + f"TwoSlabIdxGenerator(input_gro={self.input_gro}," + + f" n_atoms={self.n_atoms}," + + f" n_crystal_atoms={self.n_crystal_atoms}," + + f" verbose={self.verbose})" + ) + + def print(self) -> None: + """ + Prints the index groups and the number of atoms in each group. + """ + for key, value in self.ndx.items(): + # left justify key with 25 columns + print(f" {key:<25}: {value} atoms") + def _update_original_index(self, min_index: int, offset: int) -> None: - # update original index for all groups with offset from second slab + """ + Updates the original index for all groups with an offset from the + second slab. + + Args: + min_index (int): The minimum index of the second slab. + offset (int): The offset to be added to the indices. + + Raises: + ValueError: If the number of atoms in the System group does not + match the total number of atoms. + """ for key, value in self.ndx.items(): updated = [i + offset if i > min_index else i for i in value] self.ndx[key] = np.array(updated, dtype=int) @@ -50,12 +139,22 @@ def _update_original_index(self, min_index: int, offset: int) -> None: total_atoms = self.n_atoms if total_atoms != len(self.ndx["System"]): raise ValueError( - f"Number of atoms mismatch in System group: {total_atoms} != {len(self.ndx['System'])}" + "Number of atoms mismatch in System group:" + + f" {total_atoms} != {len(self.ndx['System'])}" ) def _add_second_slab(self, min_index: int) -> None: - # add second slab to all groups matching patterns - patterns = ["System", "non-Water", "Frozen", "Mobile", "Crystal"] + """ + Adds the second slab to all groups matching patterns. + + Args: + min_index (int): The minimum index of the second slab. + + Raises: + ValueError: If the number of atoms in the System group does not + match the total number of atoms. + """ + patterns = ["System", "non-Water", "non-Protein", "Frozen", "Mobile", "Crystal"] for key, value in self.ndx.items(): if any(p in key for p in patterns): group_new = np.array( @@ -71,25 +170,40 @@ def _add_second_slab(self, min_index: int) -> None: total_atoms = self.n_atoms + self.n_crystal_atoms if total_atoms != len(self.ndx["System"]): raise ValueError( - f"Number of atoms mismatch in System group: {total_atoms} != {len(self.ndx['System'])}" + "Number of atoms mismatch in System group:" + + f" {total_atoms} != {len(self.ndx['System'])}" ) def _sort(self) -> None: + """ + Sorts the indices in each group. + """ for key, value in self.ndx.items(): self.ndx[key] = np.sort(value) def generate(self, output_top: Path) -> None: + """ + Generates the index file for the system with two slabs. + + Args: + output_top (Path): The path to save the generated index file. + + Raises: + ValueError: If the number of atoms in the System group does not + match the total number of atoms. + """ self._update_original_index(self.n_crystal_atoms, self.n_crystal_atoms) self._add_second_slab(self.n_crystal_atoms) self._sort() - - assert self.n_atoms + self.n_crystal_atoms == max( - self.ndx["System"] - ), f"Number of atoms mismatch in System group: {self.n_atoms} != {max(self.ndx['System'])}" - self.save(output_top) def save(self, output_top: Path) -> None: + """ + Saves the index file to the specified path. + + Args: + output_top (Path): The path to save the index file. + """ self.ndx.write(output_top) @@ -112,7 +226,13 @@ def main(): args = parser.parse_args() generator = TwoSlabIdxGenerator(args.input_idx, args.input_gro, args.verbose) + if args.verbose: + print("Initial index groups:") + generator.print() generator.generate(args.output_idx) + if args.verbose: + print("Final index groups:") + generator.print() if __name__ == "__main__": diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 35b0a04..77e2b78 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -102,8 +102,6 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - # FIXME: wall-atomtype is leading to instability, may need to be removed - # sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 fi @@ -206,9 +204,6 @@ else sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1 sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1 sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1 - # FIXME: wall-atomtype is leading to instability, may need to be removed - # sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "${sim_name}.mdp" || exit 1 - # echo "wall-r-linpot = 0.1" >>"${sim_name}.mdp" || exit 1 fi # make tpr file diff --git a/scripts/method/initialization.sh b/scripts/method/initialization.sh index c5b3a6e..412c3fa 100755 --- a/scripts/method/initialization.sh +++ b/scripts/method/initialization.sh @@ -111,8 +111,6 @@ echo "INFO: Copying input files to working directory" sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "mdin.mdp" sed -i 's/^pbc .*/pbc = xy/g' "mdin.mdp" sed -i 's/^nwall .*/nwall = 2/g' "mdin.mdp" - # FIXME: this is not working - # sed -i 's/^wall-atomtype = WR WL.*/wall-atomtype = WL WL/g' "mdin.mdp" fi } >>"${log_file}" 2>&1 diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index e676365..a17533c 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -111,11 +111,9 @@ fi # ############################################################################## # Remake system topology ####################################################### # ############################################################################## - # update number of atoms in topology file if [[ -f "${archive_dir}/topol.top" ]]; then echo "DEBUG: Topology file already updated" - else echo "DEBUG: Updating topology file" { @@ -123,7 +121,7 @@ else grep -A 1000 "molecules" topol.top >temp.txt n_mol_slab="$(grep "Ion_chain_X" temp.txt | awk '{print $2}')" n_mol_2slab="$(echo "2 * ${n_mol_slab}" | bc)" - sed -i "s/${n_mol_slab}/${n_mol_2slab}/" temp.txt + sed -i "s/Ion_chain_X.*/Ion_chain_X ${n_mol_2slab}/" temp.txt # replace [ molecules ] and following in topol.top sed -i '/molecules/,$d' topol.top cat temp.txt >>topol.top @@ -138,34 +136,21 @@ fi # ############################################################################## # Remake system index ########################################################## # ############################################################################## - -# Current groups: - if [[ -f "${archive_dir}/index.ndx" ]]; then echo "DEBUG: Index file already updated" else - # call python script to update index file - echo "DEBUG: Updating index file" - cp -np "index.ndx" "${archive_dir}/index_1slab.ndx" || exit 1 - "${GMX_BIN}" make_ndx \ - -f "${sim_name}.gro" \ - -n "index.ndx" \ - -o "index.ndx" <>"${log_file}" 2>&1 fi + +# ############################################################################## +# Clean up ##################################################################### +# ############################################################################## +# delete all backup files +find . -type f -name '#*#' -delete || true From 64078ca037f2adbaffb32e7bfc5e2932935e77db Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Thu, 7 Mar 2024 07:52:28 -0800 Subject: [PATCH 10/11] Update hardware configuration in submission scripts --- submission/1eqbm_7.sh | 2 +- .../1.0_104calcite_9nm_crystal_10nm_height.sh | 6 +++--- .../input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/submission/1eqbm_7.sh b/submission/1eqbm_7.sh index af3c30d..50c53ea 100755 --- a/submission/1eqbm_7.sh +++ b/submission/1eqbm_7.sh @@ -5,7 +5,7 @@ # Slurm: Node configuration #SBATCH --partition=all --qos=dow --account=dow -#SBATCH --nodes=1 --ntasks-per-node=16 --mem=4G +#SBATCH --nodes=1 --ntasks-per-node=8 --mem=4G #SBATCH --gres=gpu:1 --gpu-bind=closest # Slurm: Runtime I/O diff --git a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index e6fb3f6..7073cd1 100755 --- a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -8,9 +8,9 @@ # Hardware #################################################################### -export CPU_THREADS='4' # number of CPU threads to use (-1 = all available) -export PIN_OFFSET='0' # offset for CPU thread pinning (-1 = no offset) -export GPU_IDS='0' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) +export CPU_THREADS='-1' # number of CPU threads to use (-1 = all available) +export PIN_OFFSET='-1' # offset for CPU thread pinning (-1 = no offset) +export GPU_IDS='-1' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) # System components ########################################################### diff --git a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh index e30becb..4e63bd1 100755 --- a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh @@ -8,9 +8,9 @@ # Hardware #################################################################### -export CPU_THREADS='4' # number of CPU threads to use (-1 = all available) -export PIN_OFFSET='4' # offset for CPU thread pinning (-1 = no offset) -export GPU_IDS='2' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) +export CPU_THREADS='1' # number of CPU threads to use (-1 = all available) +export PIN_OFFSET='1' # offset for CPU thread pinning (-1 = no offset) +export GPU_IDS='1' # GPU device(s) to use (0 = first GPU, 01 = first two GPUs) # System components ########################################################### From b12022c7408463086ad06097f055405d0bba2a31 Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Thu, 7 Mar 2024 12:33:18 -0800 Subject: [PATCH 11/11] Add second slab and update topology and index files --- scripts/utilities/second_slab.sh | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index a17533c..322bec1 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -25,8 +25,8 @@ project_path="${script_path}/../.." if [[ -f "${archive_dir}/${sim_name}_2slab.gro" ]]; then echo "DEBUG: Second slab already added" else + echo "INFO: Adding second slab to box" { - echo "DEBUG: Adding second slab to box" # copy crystal.pdb from initialization cp -np "../1-energy-minimization/crystal.gro" "crystal.gro" || exit 1 @@ -115,7 +115,7 @@ fi if [[ -f "${archive_dir}/topol.top" ]]; then echo "DEBUG: Topology file already updated" else - echo "DEBUG: Updating topology file" + echo "INFO: Updating topology file" { # get all lines [ molecules ] and following from topol.top grep -A 1000 "molecules" topol.top >temp.txt @@ -139,8 +139,10 @@ fi if [[ -f "${archive_dir}/index.ndx" ]]; then echo "DEBUG: Index file already updated" else + echo "INFO: Updating index file" + echo "DEBUG: Python exe: $(which python)" { - python3 "${project_path}/python/twoslab_index.py" \ + python "${project_path}/python/twoslab_index.py" \ -i "index.ndx" \ -g "${sim_name}.gro" \ -o "index.ndx" \