Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix383 #1

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
Open

Fix383 #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
dfc6932
fix terminals
fgrunewald Nov 21, 2024
5d69fc9
ff output
fgrunewald Nov 21, 2024
5d25455
fix bug and include checking util
fgrunewald Nov 21, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
845 changes: 845 additions & 0 deletions OPLS_test.ff
View file
Open in desktop

Large diffs are not rendered by default.

237 changes: 237 additions & 0 deletions assets/coord.pdb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,237 @@
TITLE smiles_molecule
REMARK THIS IS A SIMULATION BOX
CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 H0 Hter 1 45.730 44.240 58.780 1.00 0.00
ATOM 2 H15 STY 2 45.720 46.620 55.960 1.00 0.00
ATOM 3 C0 STY 2 45.780 45.080 58.070 1.00 0.00
ATOM 4 C1 STY 2 45.350 46.400 58.750 1.00 0.00
ATOM 5 C2 STY 2 45.460 47.650 57.870 1.00 0.00
ATOM 6 C3 STY 2 45.390 48.920 58.470 1.00 0.00
ATOM 7 C4 STY 2 45.480 50.090 57.710 1.00 0.00
ATOM 8 C5 STY 2 45.660 50.010 56.320 1.00 0.00
ATOM 9 C6 STY 2 45.750 48.750 55.700 1.00 0.00
ATOM 10 C7 STY 2 45.650 47.580 56.470 1.00 0.00
ATOM 11 H8 STY 2 46.810 45.150 57.710 1.00 0.00
ATOM 12 H9 STY 2 45.140 44.830 57.220 1.00 0.00
ATOM 13 H10 STY 2 46.090 46.530 59.550 1.00 0.00
ATOM 14 H11 STY 2 45.250 49.010 59.550 1.00 0.00
ATOM 15 H12 STY 2 45.410 51.070 58.190 1.00 0.00
ATOM 16 H13 STY 2 45.740 50.920 55.720 1.00 0.00
ATOM 17 H14 STY 2 45.900 48.690 54.630 1.00 0.00
ATOM 18 H15 STY 3 42.700 45.860 55.920 1.00 0.00
ATOM 19 C0 STY 3 43.990 46.280 59.520 1.00 0.00
ATOM 20 C1 STY 3 42.650 46.180 58.720 1.00 0.00
ATOM 21 C2 STY 3 42.570 44.900 57.870 1.00 0.00
ATOM 22 C3 STY 3 42.460 43.660 58.530 1.00 0.00
ATOM 23 C4 STY 3 42.390 42.460 57.800 1.00 0.00
ATOM 24 C5 STY 3 42.420 42.490 56.390 1.00 0.00
ATOM 25 C6 STY 3 42.530 43.720 55.730 1.00 0.00
ATOM 26 C7 STY 3 42.600 44.920 56.460 1.00 0.00
ATOM 27 H8 STY 3 44.050 45.400 60.170 1.00 0.00
ATOM 28 H9 STY 3 43.920 47.120 60.220 1.00 0.00
ATOM 29 H10 STY 3 41.870 46.060 59.490 1.00 0.00
ATOM 30 H11 STY 3 42.430 43.620 59.610 1.00 0.00
ATOM 31 H12 STY 3 42.300 41.510 58.320 1.00 0.00
ATOM 32 H13 STY 3 42.360 41.570 55.830 1.00 0.00
ATOM 33 H14 STY 3 42.550 43.750 54.640 1.00 0.00
ATOM 34 H4 ETH 4 41.320 47.240 57.360 1.00 0.00
ATOM 35 H5 ETH 4 42.980 47.780 57.240 1.00 0.00
ATOM 36 H6 ETH 4 42.680 48.830 59.580 1.00 0.00
ATOM 37 H7 ETH 4 40.980 48.390 59.480 1.00 0.00
ATOM 38 H8 ETH 4 42.520 50.350 57.680 1.00 0.00
ATOM 39 H9 ETH 4 40.900 49.770 57.280 1.00 0.00
ATOM 40 H10 ETH 4 40.670 51.930 58.360 1.00 0.00
ATOM 41 H11 ETH 4 40.000 50.690 59.390 1.00 0.00
ATOM 42 C0 ETH 4 42.210 47.470 57.960 1.00 0.00
ATOM 43 C1 ETH 4 41.860 48.660 58.880 1.00 0.00
ATOM 44 C2 ETH 4 41.580 49.980 58.120 1.00 0.00
ATOM 45 C3 ETH 4 40.950 51.080 59.000 1.00 0.00
ATOM 46 H4 ETH 5 42.630 50.880 60.400 1.00 0.00
ATOM 47 H5 ETH 5 42.370 52.490 59.800 1.00 0.00
ATOM 48 H6 ETH 5 40.290 52.710 61.190 1.00 0.00
ATOM 49 H7 ETH 5 41.750 52.480 62.140 1.00 0.00
ATOM 50 H8 ETH 5 39.760 51.200 62.990 1.00 0.00
ATOM 51 H9 ETH 5 39.740 50.240 61.520 1.00 0.00
ATOM 52 H10 ETH 5 42.170 49.530 62.120 1.00 0.00
ATOM 53 H11 ETH 5 41.900 50.280 63.680 1.00 0.00
ATOM 54 C0 ETH 5 41.840 51.600 60.160 1.00 0.00
ATOM 55 C1 ETH 5 41.070 51.970 61.450 1.00 0.00
ATOM 56 C2 ETH 5 40.400 50.790 62.200 1.00 0.00
ATOM 57 C3 ETH 5 41.390 49.790 62.840 1.00 0.00
ATOM 58 H11 BUT 6 37.090 48.190 65.730 1.00 0.00
ATOM 59 H4 BUT 6 41.600 47.820 63.670 1.00 0.00
ATOM 60 H5 BUT 6 40.330 47.950 62.460 1.00 0.00
ATOM 61 H6 BUT 6 39.920 49.490 65.000 1.00 0.00
ATOM 62 H7 BUT 6 38.200 49.470 63.170 1.00 0.00
ATOM 63 H8 BUT 6 37.960 47.760 63.410 1.00 0.00
ATOM 64 H9 BUT 6 37.450 49.920 65.540 1.00 0.00
ATOM 65 H10 BUT 6 36.210 49.150 64.530 1.00 0.00
ATOM 66 C0 BUT 6 40.770 48.450 63.330 1.00 0.00
ATOM 67 C1 BUT 6 39.700 48.550 64.470 1.00 0.00
ATOM 68 C2 BUT 6 38.250 48.680 63.930 1.00 0.00
ATOM 69 C3 BUT 6 37.190 49.010 65.000 1.00 0.00
ATOM 70 H11 BUT 7 39.860 43.220 64.400 1.00 0.00
ATOM 71 H4 BUT 7 40.910 47.370 65.840 1.00 0.00
ATOM 72 H5 BUT 7 39.350 47.810 66.470 1.00 0.00
ATOM 73 H6 BUT 7 38.230 46.090 65.110 1.00 0.00
ATOM 74 H7 BUT 7 39.650 45.990 63.130 1.00 0.00
ATOM 75 H8 BUT 7 41.030 45.410 64.060 1.00 0.00
ATOM 76 H9 BUT 7 38.430 43.860 63.530 1.00 0.00
ATOM 77 H10 BUT 7 39.970 43.630 62.680 1.00 0.00
ATOM 78 C0 BUT 7 39.860 47.440 65.570 1.00 0.00
ATOM 79 C1 BUT 7 39.310 46.000 65.280 1.00 0.00
ATOM 80 C2 BUT 7 39.940 45.370 63.990 1.00 0.00
ATOM 81 C3 BUT 7 39.520 43.930 63.640 1.00 0.00
ATOM 82 H15 STY 8 38.210 45.570 69.170 1.00 0.00
ATOM 83 C0 STY 8 39.520 45.090 66.530 1.00 0.00
ATOM 84 C1 STY 8 38.370 44.070 66.800 1.00 0.00
ATOM 85 C2 STY 8 37.140 44.680 67.500 1.00 0.00
ATOM 86 C3 STY 8 35.860 44.480 66.940 1.00 0.00
ATOM 87 C4 STY 8 34.720 45.000 67.570 1.00 0.00
ATOM 88 C5 STY 8 34.830 45.710 68.770 1.00 0.00
ATOM 89 C6 STY 8 36.100 45.910 69.340 1.00 0.00
ATOM 90 C7 STY 8 37.250 45.400 68.700 1.00 0.00
ATOM 91 H8 STY 8 40.470 44.550 66.420 1.00 0.00
ATOM 92 H9 STY 8 39.650 45.720 67.420 1.00 0.00
ATOM 93 H10 STY 8 38.020 43.730 65.820 1.00 0.00
ATOM 94 H11 STY 8 35.750 43.930 66.010 1.00 0.00
ATOM 95 H12 STY 8 33.740 44.830 67.130 1.00 0.00
ATOM 96 H13 STY 8 33.950 46.100 69.260 1.00 0.00
ATOM 97 H14 STY 8 36.200 46.460 70.270 1.00 0.00
ATOM 98 H15 STY 9 38.650 43.990 71.190 1.00 0.00
ATOM 99 C0 STY 9 38.840 42.760 67.490 1.00 0.00
ATOM 100 C1 STY 9 39.590 42.910 68.840 1.00 0.00
ATOM 101 C2 STY 9 38.890 42.200 70.000 1.00 0.00
ATOM 102 C3 STY 9 38.670 40.810 69.940 1.00 0.00
ATOM 103 C4 STY 9 38.040 40.140 71.010 1.00 0.00
ATOM 104 C5 STY 9 37.620 40.870 72.140 1.00 0.00
ATOM 105 C6 STY 9 37.850 42.250 72.200 1.00 0.00
ATOM 106 C7 STY 9 38.480 42.920 71.130 1.00 0.00
ATOM 107 H8 STY 9 37.970 42.110 67.620 1.00 0.00
ATOM 108 H9 STY 9 39.500 42.230 66.790 1.00 0.00
ATOM 109 H10 STY 9 40.600 42.480 68.730 1.00 0.00
ATOM 110 H11 STY 9 38.990 40.240 69.070 1.00 0.00
ATOM 111 H12 STY 9 37.860 39.070 70.950 1.00 0.00
ATOM 112 H13 STY 9 37.130 40.360 72.960 1.00 0.00
ATOM 113 H14 STY 9 37.530 42.820 73.070 1.00 0.00
ATOM 114 H0 Hter 10 39.760 43.960 69.080 1.00 0.00
TER
ENDMDL
CONECT 3 4
CONECT 3 11
CONECT 3 12
CONECT 4 5
CONECT 4 13
CONECT 5 6
CONECT 5 10
CONECT 6 7
CONECT 6 14
CONECT 7 8
CONECT 7 15
CONECT 8 9
CONECT 8 16
CONECT 9 10
CONECT 9 17
CONECT 10 2
CONECT 19 20
CONECT 19 27
CONECT 19 28
CONECT 20 21
CONECT 20 29
CONECT 21 22
CONECT 21 26
CONECT 22 23
CONECT 22 30
CONECT 23 24
CONECT 23 31
CONECT 24 25
CONECT 24 32
CONECT 25 26
CONECT 25 33
CONECT 26 18
CONECT 42 43
CONECT 42 34
CONECT 42 35
CONECT 43 44
CONECT 43 36
CONECT 43 37
CONECT 44 45
CONECT 44 38
CONECT 44 39
CONECT 45 40
CONECT 45 41
CONECT 54 55
CONECT 54 46
CONECT 54 47
CONECT 55 56
CONECT 55 48
CONECT 55 49
CONECT 56 57
CONECT 56 50
CONECT 56 51
CONECT 57 52
CONECT 57 53
CONECT 66 67
CONECT 66 59
CONECT 66 60
CONECT 67 68
CONECT 67 61
CONECT 68 69
CONECT 68 62
CONECT 68 63
CONECT 69 64
CONECT 69 65
CONECT 69 58
CONECT 78 79
CONECT 78 71
CONECT 78 72
CONECT 79 80
CONECT 79 73
CONECT 80 81
CONECT 80 74
CONECT 80 75
CONECT 81 76
CONECT 81 77
CONECT 81 70
CONECT 83 84
CONECT 83 91
CONECT 83 92
CONECT 84 85
CONECT 84 93
CONECT 85 86
CONECT 85 90
CONECT 86 87
CONECT 86 94
CONECT 87 88
CONECT 87 95
CONECT 88 89
CONECT 88 96
CONECT 89 90
CONECT 89 97
CONECT 90 82
CONECT 99 100
CONECT 99 107
CONECT 99 108
CONECT 100 101
CONECT 100 109
CONECT 101 102
CONECT 101 106
CONECT 102 103
CONECT 102 110
CONECT 103 104
CONECT 103 111
CONECT 104 105
CONECT 104 112
CONECT 105 106
CONECT 105 113
CONECT 106 98
CONECT 3 1
CONECT 4 19
CONECT 84 99
CONECT 20 42
CONECT 45 54
CONECT 57 66
CONECT 67 78
CONECT 79 83
CONECT 100 114
119 changes: 119 additions & 0 deletions assets/md.mdp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,119 @@
;-------------------------------------------------------------------------------------------------------------------------------------------------
; Author : F. Grunewald
; Last Edited : 07.01.2021
; Force-Field : OPLS
; Solvent : TIP4P Water
; References : from virtualchemistry.org
;
;-------------------------------------------------------------------------------------------------------------------------------------------------

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =


; RUN CONTROL PARAMETERS
; --------------------------------------------------------------------------------------------------------------------------------------------------
integrator = md ; for equilibriation this is OK
tinit = 0 ; default
dt = 0.002 ; [1]
nsteps = 1000000 ; 8 ns of sampleing time
init-step = 0 ; default
simulation-part = 1 ; defualt
comm-mode = Linear ; default
nstcomm = 100 ; [1]
comm-grps = system ; [1]

; OUTPUT CONTROL OPTIONS
; --------------------------------------------------------------------------------------------------------------------------------------------
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 0
nstcalcenergy = 100
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 1000
compressed-x-grps =


; NEIGHBORSEARCHING PARAMETERS
; -------------------------------------------------------------------------------------------------------------------------------------------------
cutoff-scheme = verlet ; should be faster at same accuracy
nstlist = 5 ; [1]
ns_type = grid ; default
pbc = xyz ; [1]
periodic-molecules = no
verlet-buffer-tolerance = 1e-6 ; non-default but should improve accuracy
rlist = 1.1 ; default


; OPTIONS FOR ELECTROSTATICS AND VDW
; -----------------------------------------------------------------------------------------------------------------------------------------------
coulombtype = cutoff ; [1]
coulomb-modifier = Potential-shift-Verlet ;
rcoulomb-switch = 0
rcoulomb = 3
epsilon-r = 1
epsilon-rf = 1
vdw-type = cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 3 ; [1]
DispCorr = EnerPres
table-extension = 1
energygrp-table =
fourierspacing = 0.1
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_rtol_lj = 1e-03
lj-pme-comb-rule = geometric
ewald_geometry = 3d
epsilon_surface = 0


; OPTIONS FOR WEAK COUPLING ALGORITHMS
; ---------------------------------------------------------------------------------------------------------------------------------------------
tcoupl = v_rescale ; We equilibriate so this is good enough
nsttcouple = 5 ; default
nh-chain-length = 10 ; N/A
print-nose-hoover-chain-variables = no ; N/A
tc-grps = system ; For small molecules OK
tau-t = 0.1 ; N/A overwritten by SD
ref-t = 298.15 ; standard condition
pcoupl = no
pcoupltype = isotropic ; We equilibriate so this is good enough
nstpcouple = 2
tau-p = 1
compressibility = 4.5e-5
ref-p = 1
refcoord-scaling = No

; GENERATE VELOCITIES FOR STARTUP RUN
; ---------------------------------------------------------------------------------------------------------------------------------------------
gen-vel = yes ; for free energy stuff we don't want this
gen-temp = 298.15 ; N/A
gen-seed = -1 ; N/A

; OPTIONS FOR BONDS
; ---------------------------------------------------------------------------------------------------------------------------------------------
constraints = None ; [1] water is done via shake
; Type of constraint algorithm
constraint-algorithm = Lincs ; default
continuation = no ; default
Shake-SOR = no ; default
shake-tol = 0.0001 ; default also same as in [1]
lincs-order = 4 ; default
lincs-iter = 1 ; default
lincs-warnangle = 90 ; default
morse = no ; default

; Free energy variables
;----------------------------------------------------------------------------------------------------------------------------------------------
free-energy = no ; only for equilibriation
2 changes: 1 addition & 1 deletion assets/smiles_molecule_GMX_OPLS.top
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
; smiles_molecule_GMX_OPLS.top created by acpype (v: 2023.10.27) on Wed Nov 20 16:42:24 2024

; Include forcefield parameters
#include forcefield.itp
#include "forcefield.itp"

; Include smiles_molecule_GMX.itp topology
#include "smiles_molecule_GMX.itp"
Expand Down
2 changes: 2 additions & 0 deletions check.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
#!/bin/bash
python compare.py -p polyply_output/polyply.top assets/smiles_molecule_GMX_OPLS.top -c assets/coord.pdb -f assets/md.mdp
Loading