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Added input files for the anthracene system
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wehs7661 committed Apr 3, 2024
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3,236 changes: 3,236 additions & 0 deletions ensemble_md/data/anthracene/anthracene.gro
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169 changes: 169 additions & 0 deletions ensemble_md/data/anthracene/anthracene.top
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; 3d1_GMX_OPLS.itp created by acpypi (Rev: 250) on Wed Sep 23 14:49:10 2009
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5



[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
CH CA 13.019 0 A 3.74119144658246e-01 0.502658843994140e+00 ;
C CA 12.011 0 A 3.36109739624996e-01 0.405868318433803e+00 ;
DUM CA 12.011 0.000 A 0 0


[ bondtypes ]


[ angletypes ]


[ dihedraltypes ]


[ atomtypes ]
opls_111 OW 15.99940 0.000 A 3.15061e-01 6.363864e-01
opls_112 HW 1.00800 0.000 A 0.00000e-01 0.000000e-01

[ moleculetype ]
; molname nrexcl
SOL 1

[ atoms ]
1 opls_111 1 SOL OW 1 -0.834
2 opls_112 1 SOL HW1 1 0.417
3 opls_112 1 SOL HW2 1 0.417

[ settles ]
; i j funct length
1 1 0.09572 0.15139

[ exclusions ]
1 2 3
2 1 3
3 1 2


[ moleculetype ]
;name nrexcl
COM 3

[ atoms ]
; nr type resinr residue atom cgnr charge mass
1 CH 1 COM C1 1 0 13.01900
2 CH 1 COM C2 2 0 13.01900
3 CH 1 COM C5 5 0 13.01900
4 CH 1 COM C6 6 0 13.01900
5 CH 1 COM C9 9 0 13.01900
6 CH 1 COM C10 10 0 13.01900
7 CH 1 COM C13 13 0 13.01900
8 CH 1 COM C14 14 0 13.01900
9 C 1 COM C15 15 0 12.01100
10 C 1 COM C16 16 0 12.01100
11 C 1 COM C19 19 0 12.01100
12 C 1 COM C20 20 0 12.01100
13 CH 1 COM C21 21 0 13.01900
14 CH 1 COM C22 22 0 13.01900

[ bonds ]
; ai aj funct r k
1 2 1 1.3900e-01 417333.6 ; C1 - C2 -
1 3 1 1.3900e-01 417333.6 ; C1 - C5 -
2 4 1 1.3900e-01 417333.6 ; C2 - C6 -
3 9 1 1.3900e-01 417333.6 ; C5 - C15 -
4 10 1 1.3900e-01 417333.6 ; C6 - C16 -
5 9 1 1.3900e-01 417333.6 ; C9 - C15 -
5 11 1 1.3900e-01 417333.6 ; C9 - C19 -
6 10 1 1.3900e-01 417333.6 ; C10 - C16 -
6 12 1 1.3900e-01 417333.6 ; C10 - C20 -
7 11 1 1.3900e-01 417333.6 ; C13 - C19 -
7 13 1 1.3900e-01 417333.6 ; C13 - C21 -
8 12 1 1.3900e-01 417333.6 ; C14 - C20 -
8 14 1 1.3900e-01 417333.6 ; C14 - C22 -
9 10 1 1.3900e-01 417333.6 ; C15 - C16 -
11 12 1 1.3900e-01 417333.6 ; C19 - C20 -
13 14 1 1.3900e-01 417333.6 ; C21 - C22 -

[ pairs ]
; ai aj funct
1 5 1 ; C1 - C9
1 10 1 ; C1 - C16
2 6 1 ; C2 - C10
2 9 1 ; C2 - C15
3 4 1 ; C5 - C6
3 6 1 ; C5 - C10
3 11 1 ; C5 - C19
4 5 1 ; C6 - C9
4 12 1 ; C6 - C20
5 6 1 ; C9 - C10
5 8 1 ; C9 - C14
5 13 1 ; C9 - C21
6 7 1 ; C10 - C13
6 14 1 ; C10 - C22
7 8 1 ; C13 - C14
7 9 1 ; C13 - C15
8 10 1 ; C14 - C16
9 12 1 ; C15 - C20
10 11 1 ; C16 - C19
11 14 1 ; C19 - C22
12 13 1 ; C20 - C21

[ angles ]
; ai aj ak funct theta cth
1 2 4 1 1.2000e+02 4.2000e+02 ; C1 - C2 - C6 - -
1 3 9 1 1.2000e+02 4.2000e+02 ; C1 - C5 - C15 - -
2 1 3 1 1.2000e+02 4.2000e+02 ; C2 - C1 - C5 - -
2 4 10 1 1.2000e+02 4.2000e+02 ; C2 - C6 - C16 - -
3 9 5 1 1.2000e+02 4.2000e+02 ; C5 - C15 - C9 - -
3 9 10 1 1.2000e+02 4.2000e+02 ; C5 - C15 - C16 - -
4 10 6 1 1.2000e+02 4.2000e+02 ; C6 - C16 - C10 - -
4 10 9 1 1.2000e+02 4.2000e+02 ; C6 - C16 - C15 - -
5 9 10 1 1.2000e+02 4.2000e+02 ; C9 - C15 - C16 - -
5 11 7 1 1.2000e+02 4.2000e+02 ; C9 - C19 - C13 - -
5 11 12 1 1.2000e+02 4.2000e+02 ; C9 - C19 - C20 - -
6 10 9 1 1.2000e+02 4.2000e+02 ; C10 - C16 - C15 - -
6 12 8 1 1.2000e+02 4.2000e+02 ; C10 - C20 - C14 - -
6 12 11 1 1.2000e+02 4.2000e+02 ; C10 - C20 - C19 - -
7 11 12 1 1.2000e+02 4.2000e+02 ; C13 - C19 - C20 - -
7 13 14 1 1.2000e+02 4.2000e+02 ; C13 - C21 - C22 - -
8 12 11 1 1.2000e+02 4.2000e+02 ; C14 - C20 - C19 - -
8 14 13 1 1.2000e+02 4.2000e+02 ; C14 - C22 - C21 - -
9 5 11 1 1.2000e+02 4.2000e+02 ; C15 - C9 - C19 - -
10 6 12 1 1.2000e+02 4.2000e+02 ; C16 - C10 - C20 - -
11 7 13 1 1.2000e+02 4.2000e+02 ; C19 - C13 - C21 - -
12 8 14 1 1.2000e+02 4.2000e+02 ; C20 - C14 - C22 - -


[ dihedrals ] ; impropers
; i j k l func phase kd
3 5 9 10 2 180 167.4231 ; C5- C9- C15- C16
4 6 10 9 2 180 167.4231 ; C6- C10- C16- C15
5 7 11 12 2 180 167.4231 ; C9- C13- C19- C20
6 8 12 11 2 180 167.4231 ; C10- C14- C20- C19
3 2 1 4 2 0 167.4231 ; C5 C2 C1 C6 added
1 4 2 10 2 0 167.4231 ; C1 C6 C2 C16 added
2 10 4 9 2 0 167.4231 ; C2 C16 C6 C15 added
4 9 10 3 2 0 167.4231 ; C6 C15 C16 C5 added
10 3 9 1 2 0 167.4231 ; C16 C5 C15 C1 added
9 1 3 2 2 0 167.4231 ; C15 C1 C5 C2 added
5 10 9 6 2 0 167.4231 ; C9 C16 C15 C10 added
9 6 10 12 2 0 167.4231 ; C15 C10 C16 C20 added
10 12 6 11 2 0 167.4231 ; C16 C20 C10 C19 added
6 11 12 5 2 0 167.4231 ; C10 C19 C20 C9 added
12 5 11 9 2 0 167.4231 ; C20 C9 C19 C15 added
11 9 5 10 2 0 167.4231 ; C19 C15 C9 C16 added
7 12 11 8 2 0 167.4231 ; C13 C20 C19 C14 added
11 8 12 14 2 0 167.4231 ; C19 C14 C20 C22 added
12 14 8 13 2 0 167.4231 ; C20 C22 C14 C21 added
8 13 14 7 2 0 167.4231 ; C14 C21 C22 C13 added
14 7 13 11 2 0 167.4231 ; C22 C13 C21 C19 added
13 11 7 12 2 0 167.4231 ; C21 C19 C13 C20 added

[ system ]
; Name
Anthracene Benzene Null Transform in water

[ molecules ]
; Compound #mols
COM 1
SOL 1073
100 changes: 100 additions & 0 deletions ensemble_md/data/anthracene/fixed_weight.mdp
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; Run control
integrator = md-vv
tinit = 0
dt = 0.002
nsteps = 100000000
comm_mode = Linear
nstcomm = 1
nstfout = 0

; Output control
nstlog = 1000
nstcalcenergy = 1
nstenergy = 1000
nstxout_compressed = 1000

; Neighborsearching and short-range nonbonded interactions
nstlist = 10
pbc = xyz
rlist = 1.0

; Electrostatics
coulombtype = PME
rcoulomb = 0.9

; van der Waals
vdwtype = Cut-off
vdw_modifier = Potential-switch
rvdw_switch = 0.8
rvdw = 0.9

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = AllEnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.1

; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
ewald_geometry = 3d
epsilon_surface = 0

; Temperature coupling
tcoupl = v-rescale
tc_grps = System
tau_t = 2.0
ref_t = 300

; Pressure coupling is on for NPT
pcoupl = no

; refcoord_scaling should do nothing since there are no position restraints.
gen_vel = yes
gen_temp = 300
gen_seed = -1

; options for bonds
constraints = h-bonds

; Type of constraint algorithm
constraint_algorithm = lincs

; Highest order in the expansion of the constraint coupling matrix
lincs_order = 4
lincs_iter = 2
continuation = no

; Free energy calculation
free_energy = expanded
calc_lambda_neighbors = -1
sc_alpha = 0.5
sc_power = 1
couple_moltype = COM
couple_lambda0 = vdw
couple_lambda1 = none
couple_intramol = no
init_lambda_state = 0
nstdhdl = 100
dhdl_print_energy = total

; Seed for Monte Carlo in lambda space
lmc_seed = -1
lmc_gibbsdelta = -1
lmc_forced_nstart = 0
symmetrized_transition_matrix = no
nst_transition_matrix = 100000
; wl-scale = 0.8
; wl-ratio = 0.8
; init-wl-delta = 0.5

; expanded ensemble variables
nstexpanded = 100
lmc_stats = no
lmc_move = metropolized-gibbs
; lmc-weights-equil = wl-delta
; weight-equil-wl-delta = 0.001

; lambda-states = 1 2 3 4 5 6 7 8
vdw_lambdas = 0.0 0.18 0.42 0.57 0.68 0.76 0.86 1.0
init_lambda_weights = 0.0 4.32298 9.25799 11.45557 11.88643 10.43653 6.22252 3.39715
101 changes: 101 additions & 0 deletions ensemble_md/data/anthracene/md.mdp
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; Run control
integrator = md-vv
tinit = 0
dt = 0.002
nsteps = 12500000 ; 25 ns
comm-mode = Linear
nstcomm = 1
nstfout = 0

; Output control
nstlog = 1000
nstcalcenergy = 1
nstenergy = 1000
nstxout-compressed = 1000

; Neighborsearching and short-range nonbonded interactions
nstlist = 10
pbc = xyz
rlist = 1.0

; Electrostatics
coulombtype = PME
rcoulomb = 0.9

; van der Waals
vdw-type = Cut-off
vdw_modifier = Potential-switch
rvdw-switch = 0.8
rvdw = 0.9

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = AllEnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.10

; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
ewald_geometry = 3d
epsilon_surface = 0

; Temperature coupling
tcoupl = v-rescale
tc_grps = System
tau_t = 2.0
ref_t = 300

; Pressure coupling is on for NPT
pcoupl = no

; refcoord_scaling should do nothing since there are no position restraints.

gen_vel = yes
gen-temp = 300
gen-seed = -1; need to randomize the seed each time.

; options for bonds
constraints = h-bonds ; we only have C-H bonds here

; Type of constraint algorithm
constraint-algorithm = lincs
continuation = no

; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
lincs-iter = 2

; Free energy calculation
free_energy = yes
calc-lambda-neighbors = -1
sc-alpha = 0.5
sc-power = 1
couple-moltype = COM
couple-lambda0 = vdw
couple-lambda1 = none
couple-intramol = no
init-lambda-state = 0

nstdhdl = 100
dhdl-print-energy = total

; Seed for Monte Carlo in lambda space
; lmc-seed = 1000
; lmc-gibbsdelta = -1
; lmc-forced-nstart = 0
; symmetrized-transition-matrix = no
; nst-transition-matrix = 100000
;wl-scale = 0.8
;wl-ratio = 0.8
;init-wl-delta = 0.5

; expanded ensemble variables
; nstexpanded = 10
; lmc-stats = no
; lmc-move = metropolized-gibbs
;lmc-weights-equil = wl-delta
; weight-equil-wl-delta = 0.001

; lambda-states = 1 2 3 4 5 6 7 8
vdw-lambdas = 0.00 0.18 0.42 0.57 0.68 0.76 0.86 1.00
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