From 600d56b13cb7c167b6f600f78712490fc143e679 Mon Sep 17 00:00:00 2001 From: jimboid Date: Thu, 8 Sep 2016 14:27:18 +0100 Subject: [PATCH] Moved examples Moved the examples out of the package and up into the top level, this should be beneficial for preparing packages for release. --- .../CondorSubmission/condor_desc | 0 .../CondorSubmission/example.in | 0 .../CondorSubmission/example.min | 0 .../CondorSubmission/example.top | 0 .../MultipleJobs/MultipleJobTypes/job.conf | 0 .../MultipleJobTypes/replicate/example.rst | 0 .../MultipleJobTypes/replicate/example.top | 0 .../MultipleJobTypes/replicate/rep1/example.in | 0 .../MultipleJobTypes/replicate/rep2/example.in | 0 .../MultipleJobTypes/replicate/rep3/example.in | 0 .../MultipleJobTypes/replicate/rep4/example.in | 0 .../MultipleJobTypes/replicate/rep5/example.in | 0 .../MultipleJobs/MultipleJobTypes/single/example.in | 0 .../MultipleJobTypes/single/example.rst | 0 .../MultipleJobTypes/single/example.top | 0 .../amber/example.in | 0 .../amber/example.rst | 0 .../amber/example.top | 0 .../gromacs_d/example.tpr | Bin .../gromacs_s/example.tpr | Bin .../MultipleJobsDifferentApplications/job.conf | 0 .../lammps/example.data | 0 .../lammps/example.in | 0 .../namd/example.in | 0 .../namd/par_all27_prot_lipid.prm | 0 .../namd/relres.coor | Bin .../namd/relres.vel | Bin .../namd/relres.xsc | 0 .../namd/solvated.pdb | 0 .../namd/solvated.psf | 0 .../QuickStart/Amber/example.in | 0 .../QuickStart/Amber/example.min | 0 .../QuickStart/Amber/example.top | 0 .../QuickStart/CHARMM/example.crd | 0 .../QuickStart/CHARMM/example.inp | 0 .../QuickStart/CHARMM/example.psf | 0 .../QuickStart/CHARMM/example.rst | 0 .../QuickStart/CHARMM/par_all27_prot_lipid.prm | 0 .../QuickStart/CHARMM/top_all27_prot_lipid.rtf | 0 .../QuickStart/Gromacs/3NIR.top | 0 .../QuickStart/Gromacs/_example.mdp | 0 .../QuickStart/Gromacs/example.tpr | Bin .../QuickStart/LAMMPS/example.data | 0 .../QuickStart/LAMMPS/example.in | 0 .../QuickStart/NAMD/example.in | 0 .../QuickStart/NAMD/par_all27_prot_lipid.prm | 0 .../QuickStart/NAMD/relres.coor | Bin .../QuickStart/NAMD/relres.vel | Bin .../QuickStart/NAMD/relres.xsc | 0 .../QuickStart/NAMD/solvated.pdb | 0 .../QuickStart/NAMD/solvated.psf | 0 {Longbow/LongbowExamples => Examples}/README | 0 .../ReplicateJob/par_all27_prot_lipid.prm | 0 .../ReplicateJob/rep1/example.in | 0 .../ReplicateJob/rep1/relres.coor | Bin .../ReplicateJob/rep1/relres.vel | Bin .../ReplicateJob/rep1/relres.xsc | 0 .../ReplicateJob/rep2/example.in | 0 .../ReplicateJob/rep2/relres.coor | Bin .../ReplicateJob/rep2/relres.vel | Bin .../ReplicateJob/rep2/relres.xsc | 0 .../ReplicateJob/rep3/example.in | 0 .../ReplicateJob/rep3/relres.coor | Bin .../ReplicateJob/rep3/relres.vel | Bin .../ReplicateJob/rep3/relres.xsc | 0 .../ReplicateJob/rep4/example.in | 0 .../ReplicateJob/rep4/relres.coor | Bin .../ReplicateJob/rep4/relres.vel | Bin .../ReplicateJob/rep4/relres.xsc | 0 .../ReplicateJob/rep5/example.in | 0 .../ReplicateJob/rep5/relres.coor | Bin .../ReplicateJob/rep5/relres.vel | Bin .../ReplicateJob/rep5/relres.xsc | 0 .../ReplicateJob/solvated.pdb | 0 .../ReplicateJob/solvated.psf | 0 {Longbow/LongbowExamples => Examples}/how-to-run | 0 76 files changed, 0 insertions(+), 0 deletions(-) rename {Longbow/LongbowExamples => Examples}/CondorSubmission/condor_desc (100%) rename {Longbow/LongbowExamples => Examples}/CondorSubmission/example.in (100%) rename {Longbow/LongbowExamples => Examples}/CondorSubmission/example.min (100%) rename {Longbow/LongbowExamples => Examples}/CondorSubmission/example.top (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/job.conf (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/example.rst (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/example.top (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/rep1/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/rep2/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/rep3/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/rep4/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/replicate/rep5/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/single/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/single/example.rst (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobTypes/single/example.top (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/amber/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/amber/example.rst (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/amber/example.top (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/gromacs_d/example.tpr (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/gromacs_s/example.tpr (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/job.conf (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.data (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/example.in (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/par_all27_prot_lipid.prm (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.pdb (100%) rename {Longbow/LongbowExamples => Examples}/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.psf (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/Amber/example.in (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/Amber/example.min (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/Amber/example.top (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/CHARMM/example.crd (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/CHARMM/example.inp (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/CHARMM/example.psf (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/CHARMM/example.rst (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/CHARMM/par_all27_prot_lipid.prm (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/CHARMM/top_all27_prot_lipid.rtf (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/Gromacs/3NIR.top (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/Gromacs/_example.mdp (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/Gromacs/example.tpr (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/LAMMPS/example.data (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/LAMMPS/example.in (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/example.in (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/par_all27_prot_lipid.prm (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/solvated.pdb (100%) rename {Longbow/LongbowExamples => Examples}/QuickStart/NAMD/solvated.psf (100%) rename {Longbow/LongbowExamples => Examples}/README (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/par_all27_prot_lipid.prm (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep1/example.in (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep1/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep1/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep1/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep2/example.in (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep2/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep2/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep2/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep3/example.in (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep3/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep3/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep3/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep4/example.in (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep4/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep4/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep4/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep5/example.in (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep5/relres.coor (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep5/relres.vel (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/rep5/relres.xsc (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/solvated.pdb (100%) rename {Longbow/LongbowExamples => Examples}/ReplicateJob/solvated.psf (100%) rename {Longbow/LongbowExamples => Examples}/how-to-run (100%) diff --git a/Longbow/LongbowExamples/CondorSubmission/condor_desc b/Examples/CondorSubmission/condor_desc similarity index 100% rename from Longbow/LongbowExamples/CondorSubmission/condor_desc rename to Examples/CondorSubmission/condor_desc diff --git a/Longbow/LongbowExamples/CondorSubmission/example.in b/Examples/CondorSubmission/example.in similarity index 100% rename from Longbow/LongbowExamples/CondorSubmission/example.in rename to Examples/CondorSubmission/example.in diff --git a/Longbow/LongbowExamples/CondorSubmission/example.min b/Examples/CondorSubmission/example.min similarity index 100% rename from Longbow/LongbowExamples/CondorSubmission/example.min rename to Examples/CondorSubmission/example.min diff --git a/Longbow/LongbowExamples/CondorSubmission/example.top b/Examples/CondorSubmission/example.top similarity index 100% rename from Longbow/LongbowExamples/CondorSubmission/example.top rename to Examples/CondorSubmission/example.top diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/job.conf b/Examples/MultipleJobs/MultipleJobTypes/job.conf similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/job.conf rename to Examples/MultipleJobs/MultipleJobTypes/job.conf diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/example.rst b/Examples/MultipleJobs/MultipleJobTypes/replicate/example.rst similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/example.rst rename to Examples/MultipleJobs/MultipleJobTypes/replicate/example.rst diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/example.top b/Examples/MultipleJobs/MultipleJobTypes/replicate/example.top similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/example.top rename to Examples/MultipleJobs/MultipleJobTypes/replicate/example.top diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep1/example.in b/Examples/MultipleJobs/MultipleJobTypes/replicate/rep1/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep1/example.in rename to Examples/MultipleJobs/MultipleJobTypes/replicate/rep1/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep2/example.in b/Examples/MultipleJobs/MultipleJobTypes/replicate/rep2/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep2/example.in rename to Examples/MultipleJobs/MultipleJobTypes/replicate/rep2/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep3/example.in b/Examples/MultipleJobs/MultipleJobTypes/replicate/rep3/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep3/example.in rename to Examples/MultipleJobs/MultipleJobTypes/replicate/rep3/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep4/example.in b/Examples/MultipleJobs/MultipleJobTypes/replicate/rep4/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep4/example.in rename to Examples/MultipleJobs/MultipleJobTypes/replicate/rep4/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep5/example.in b/Examples/MultipleJobs/MultipleJobTypes/replicate/rep5/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/replicate/rep5/example.in rename to Examples/MultipleJobs/MultipleJobTypes/replicate/rep5/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/single/example.in b/Examples/MultipleJobs/MultipleJobTypes/single/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/single/example.in rename to Examples/MultipleJobs/MultipleJobTypes/single/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/single/example.rst b/Examples/MultipleJobs/MultipleJobTypes/single/example.rst similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/single/example.rst rename to Examples/MultipleJobs/MultipleJobTypes/single/example.rst diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/single/example.top b/Examples/MultipleJobs/MultipleJobTypes/single/example.top similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobTypes/single/example.top rename to Examples/MultipleJobs/MultipleJobTypes/single/example.top diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.in b/Examples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.in rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.rst b/Examples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.rst similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.rst rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.rst diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.top b/Examples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.top similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.top rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/amber/example.top diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_d/example.tpr b/Examples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_d/example.tpr similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_d/example.tpr rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_d/example.tpr diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_s/example.tpr b/Examples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_s/example.tpr similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_s/example.tpr rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/gromacs_s/example.tpr diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/job.conf b/Examples/MultipleJobs/MultipleJobsDifferentApplications/job.conf similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/job.conf rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/job.conf diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.data b/Examples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.data similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.data rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.data diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.in b/Examples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.in rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/lammps/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/example.in b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/example.in similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/example.in rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/example.in diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/par_all27_prot_lipid.prm b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/par_all27_prot_lipid.prm similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/par_all27_prot_lipid.prm rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/par_all27_prot_lipid.prm diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.coor b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.coor similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.coor rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.coor diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.vel b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.vel similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.vel rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.vel diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.xsc b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.xsc rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/relres.xsc diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.pdb b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.pdb similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.pdb rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.pdb diff --git a/Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.psf b/Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.psf similarity index 100% rename from Longbow/LongbowExamples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.psf rename to Examples/MultipleJobs/MultipleJobsDifferentApplications/namd/solvated.psf diff --git a/Longbow/LongbowExamples/QuickStart/Amber/example.in b/Examples/QuickStart/Amber/example.in similarity index 100% rename from Longbow/LongbowExamples/QuickStart/Amber/example.in rename to Examples/QuickStart/Amber/example.in diff --git a/Longbow/LongbowExamples/QuickStart/Amber/example.min b/Examples/QuickStart/Amber/example.min similarity index 100% rename from Longbow/LongbowExamples/QuickStart/Amber/example.min rename to Examples/QuickStart/Amber/example.min diff --git a/Longbow/LongbowExamples/QuickStart/Amber/example.top b/Examples/QuickStart/Amber/example.top similarity index 100% rename from Longbow/LongbowExamples/QuickStart/Amber/example.top rename to Examples/QuickStart/Amber/example.top diff --git a/Longbow/LongbowExamples/QuickStart/CHARMM/example.crd b/Examples/QuickStart/CHARMM/example.crd similarity index 100% rename from Longbow/LongbowExamples/QuickStart/CHARMM/example.crd rename to Examples/QuickStart/CHARMM/example.crd diff --git a/Longbow/LongbowExamples/QuickStart/CHARMM/example.inp b/Examples/QuickStart/CHARMM/example.inp similarity index 100% rename from Longbow/LongbowExamples/QuickStart/CHARMM/example.inp rename to Examples/QuickStart/CHARMM/example.inp diff --git a/Longbow/LongbowExamples/QuickStart/CHARMM/example.psf b/Examples/QuickStart/CHARMM/example.psf similarity index 100% rename from Longbow/LongbowExamples/QuickStart/CHARMM/example.psf rename to Examples/QuickStart/CHARMM/example.psf diff --git a/Longbow/LongbowExamples/QuickStart/CHARMM/example.rst b/Examples/QuickStart/CHARMM/example.rst similarity index 100% rename from Longbow/LongbowExamples/QuickStart/CHARMM/example.rst rename to Examples/QuickStart/CHARMM/example.rst diff --git a/Longbow/LongbowExamples/QuickStart/CHARMM/par_all27_prot_lipid.prm b/Examples/QuickStart/CHARMM/par_all27_prot_lipid.prm similarity index 100% rename from Longbow/LongbowExamples/QuickStart/CHARMM/par_all27_prot_lipid.prm rename to Examples/QuickStart/CHARMM/par_all27_prot_lipid.prm diff --git a/Longbow/LongbowExamples/QuickStart/CHARMM/top_all27_prot_lipid.rtf b/Examples/QuickStart/CHARMM/top_all27_prot_lipid.rtf similarity index 100% rename from Longbow/LongbowExamples/QuickStart/CHARMM/top_all27_prot_lipid.rtf rename to Examples/QuickStart/CHARMM/top_all27_prot_lipid.rtf diff --git a/Longbow/LongbowExamples/QuickStart/Gromacs/3NIR.top b/Examples/QuickStart/Gromacs/3NIR.top similarity index 100% rename from Longbow/LongbowExamples/QuickStart/Gromacs/3NIR.top rename to Examples/QuickStart/Gromacs/3NIR.top diff --git a/Longbow/LongbowExamples/QuickStart/Gromacs/_example.mdp b/Examples/QuickStart/Gromacs/_example.mdp similarity index 100% rename from Longbow/LongbowExamples/QuickStart/Gromacs/_example.mdp rename to Examples/QuickStart/Gromacs/_example.mdp diff --git a/Longbow/LongbowExamples/QuickStart/Gromacs/example.tpr b/Examples/QuickStart/Gromacs/example.tpr similarity index 100% rename from Longbow/LongbowExamples/QuickStart/Gromacs/example.tpr rename to Examples/QuickStart/Gromacs/example.tpr diff --git a/Longbow/LongbowExamples/QuickStart/LAMMPS/example.data b/Examples/QuickStart/LAMMPS/example.data similarity index 100% rename from Longbow/LongbowExamples/QuickStart/LAMMPS/example.data rename to Examples/QuickStart/LAMMPS/example.data diff --git a/Longbow/LongbowExamples/QuickStart/LAMMPS/example.in b/Examples/QuickStart/LAMMPS/example.in similarity index 100% rename from Longbow/LongbowExamples/QuickStart/LAMMPS/example.in rename to Examples/QuickStart/LAMMPS/example.in diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/example.in b/Examples/QuickStart/NAMD/example.in similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/example.in rename to Examples/QuickStart/NAMD/example.in diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/par_all27_prot_lipid.prm b/Examples/QuickStart/NAMD/par_all27_prot_lipid.prm similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/par_all27_prot_lipid.prm rename to Examples/QuickStart/NAMD/par_all27_prot_lipid.prm diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/relres.coor b/Examples/QuickStart/NAMD/relres.coor similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/relres.coor rename to Examples/QuickStart/NAMD/relres.coor diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/relres.vel b/Examples/QuickStart/NAMD/relres.vel similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/relres.vel rename to Examples/QuickStart/NAMD/relres.vel diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/relres.xsc b/Examples/QuickStart/NAMD/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/relres.xsc rename to Examples/QuickStart/NAMD/relres.xsc diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/solvated.pdb b/Examples/QuickStart/NAMD/solvated.pdb similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/solvated.pdb rename to Examples/QuickStart/NAMD/solvated.pdb diff --git a/Longbow/LongbowExamples/QuickStart/NAMD/solvated.psf b/Examples/QuickStart/NAMD/solvated.psf similarity index 100% rename from Longbow/LongbowExamples/QuickStart/NAMD/solvated.psf rename to Examples/QuickStart/NAMD/solvated.psf diff --git a/Longbow/LongbowExamples/README b/Examples/README similarity index 100% rename from Longbow/LongbowExamples/README rename to Examples/README diff --git a/Longbow/LongbowExamples/ReplicateJob/par_all27_prot_lipid.prm b/Examples/ReplicateJob/par_all27_prot_lipid.prm similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/par_all27_prot_lipid.prm rename to Examples/ReplicateJob/par_all27_prot_lipid.prm diff --git a/Longbow/LongbowExamples/ReplicateJob/rep1/example.in b/Examples/ReplicateJob/rep1/example.in similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep1/example.in rename to Examples/ReplicateJob/rep1/example.in diff --git a/Longbow/LongbowExamples/ReplicateJob/rep1/relres.coor b/Examples/ReplicateJob/rep1/relres.coor similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep1/relres.coor rename to Examples/ReplicateJob/rep1/relres.coor diff --git a/Longbow/LongbowExamples/ReplicateJob/rep1/relres.vel b/Examples/ReplicateJob/rep1/relres.vel similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep1/relres.vel rename to Examples/ReplicateJob/rep1/relres.vel diff --git a/Longbow/LongbowExamples/ReplicateJob/rep1/relres.xsc b/Examples/ReplicateJob/rep1/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep1/relres.xsc rename to Examples/ReplicateJob/rep1/relres.xsc diff --git a/Longbow/LongbowExamples/ReplicateJob/rep2/example.in b/Examples/ReplicateJob/rep2/example.in similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep2/example.in rename to Examples/ReplicateJob/rep2/example.in diff --git a/Longbow/LongbowExamples/ReplicateJob/rep2/relres.coor b/Examples/ReplicateJob/rep2/relres.coor similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep2/relres.coor rename to Examples/ReplicateJob/rep2/relres.coor diff --git a/Longbow/LongbowExamples/ReplicateJob/rep2/relres.vel b/Examples/ReplicateJob/rep2/relres.vel similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep2/relres.vel rename to Examples/ReplicateJob/rep2/relres.vel diff --git a/Longbow/LongbowExamples/ReplicateJob/rep2/relres.xsc b/Examples/ReplicateJob/rep2/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep2/relres.xsc rename to Examples/ReplicateJob/rep2/relres.xsc diff --git a/Longbow/LongbowExamples/ReplicateJob/rep3/example.in b/Examples/ReplicateJob/rep3/example.in similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep3/example.in rename to Examples/ReplicateJob/rep3/example.in diff --git a/Longbow/LongbowExamples/ReplicateJob/rep3/relres.coor b/Examples/ReplicateJob/rep3/relres.coor similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep3/relres.coor rename to Examples/ReplicateJob/rep3/relres.coor diff --git a/Longbow/LongbowExamples/ReplicateJob/rep3/relres.vel b/Examples/ReplicateJob/rep3/relres.vel similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep3/relres.vel rename to Examples/ReplicateJob/rep3/relres.vel diff --git a/Longbow/LongbowExamples/ReplicateJob/rep3/relres.xsc b/Examples/ReplicateJob/rep3/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep3/relres.xsc rename to Examples/ReplicateJob/rep3/relres.xsc diff --git a/Longbow/LongbowExamples/ReplicateJob/rep4/example.in b/Examples/ReplicateJob/rep4/example.in similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep4/example.in rename to Examples/ReplicateJob/rep4/example.in diff --git a/Longbow/LongbowExamples/ReplicateJob/rep4/relres.coor b/Examples/ReplicateJob/rep4/relres.coor similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep4/relres.coor rename to Examples/ReplicateJob/rep4/relres.coor diff --git a/Longbow/LongbowExamples/ReplicateJob/rep4/relres.vel b/Examples/ReplicateJob/rep4/relres.vel similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep4/relres.vel rename to Examples/ReplicateJob/rep4/relres.vel diff --git a/Longbow/LongbowExamples/ReplicateJob/rep4/relres.xsc b/Examples/ReplicateJob/rep4/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep4/relres.xsc rename to Examples/ReplicateJob/rep4/relres.xsc diff --git a/Longbow/LongbowExamples/ReplicateJob/rep5/example.in b/Examples/ReplicateJob/rep5/example.in similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep5/example.in rename to Examples/ReplicateJob/rep5/example.in diff --git a/Longbow/LongbowExamples/ReplicateJob/rep5/relres.coor b/Examples/ReplicateJob/rep5/relres.coor similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep5/relres.coor rename to Examples/ReplicateJob/rep5/relres.coor diff --git a/Longbow/LongbowExamples/ReplicateJob/rep5/relres.vel b/Examples/ReplicateJob/rep5/relres.vel similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep5/relres.vel rename to Examples/ReplicateJob/rep5/relres.vel diff --git a/Longbow/LongbowExamples/ReplicateJob/rep5/relres.xsc b/Examples/ReplicateJob/rep5/relres.xsc similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/rep5/relres.xsc rename to Examples/ReplicateJob/rep5/relres.xsc diff --git a/Longbow/LongbowExamples/ReplicateJob/solvated.pdb b/Examples/ReplicateJob/solvated.pdb similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/solvated.pdb rename to Examples/ReplicateJob/solvated.pdb diff --git a/Longbow/LongbowExamples/ReplicateJob/solvated.psf b/Examples/ReplicateJob/solvated.psf similarity index 100% rename from Longbow/LongbowExamples/ReplicateJob/solvated.psf rename to Examples/ReplicateJob/solvated.psf diff --git a/Longbow/LongbowExamples/how-to-run b/Examples/how-to-run similarity index 100% rename from Longbow/LongbowExamples/how-to-run rename to Examples/how-to-run