set dt=0.002 for heat-press MD

freeenergylab · Aug 15, 2024 · 303e730 · 303e730
1 parent 2cc25d2
commit 303e730
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/abfe/abfe_alchemy_md.py b/abfe/abfe_alchemy_md.py
@@ -317,7 +317,7 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
         for n, (tempi, temp0) in enumerate(zip(args.heat_temps[:-1], args.heat_temps[1:]), 1):
             lig_md_steps['heat-%s'%str(n)] = SOLVATED_HEAT\
                 .replace('CLAMBDA', str(_lambda))\
-                .replace('DT', str(args.timestep))\
+                .replace('DT', str(0.002))\
                 .replace('CUT', str(args.cutoff))\
                 .replace('TEMPI', str(tempi))\
                 .replace('TEMP0', str(temp0))\
@@ -331,7 +331,7 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
                 .replace('RESTRAINTMASK', str(args.restraintmask))
             lig_md_steps['press-%s'%str(n)] = SOLVATED_PRESS\
                 .replace('CLAMBDA', str(_lambda))\
-                .replace('DT', str(args.timestep))\
+                .replace('DT', str(0.002))\
                 .replace('CUT', str(args.cutoff))\
                 .replace('TEMP0', str(temp0))\
                 .replace('GTI_ADD_SC', str(args.gti_add_sc))\
@@ -541,7 +541,7 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
             for n, (tempi, temp0) in enumerate(zip(args.heat_temps[:-1], args.heat_temps[1:]), 1):
                 comp_md_steps['heat-%s'%str(n)] = COMPLEX_HEAT\
                     .replace('CLAMBDA', str(_lambda))\
-                    .replace('DT', str(args.timestep))\
+                    .replace('DT', str(0.002))\
                     .replace('CUT', str(args.cutoff))\
                     .replace('TEMPI', str(tempi))\
                     .replace('TEMP0', str(temp0))\
@@ -555,7 +555,7 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
                     .replace('RESTRAINTMASK', str(args.restraintmask))
                 comp_md_steps['press-%s'%str(n)] = COMPLEX_PRESS\
                     .replace('CLAMBDA', str(_lambda))\
-                    .replace('DT', str(args.timestep))\
+                    .replace('DT', str(0.002))\
                     .replace('CUT', str(args.cutoff))\
                     .replace('TEMP0', str(temp0))\
                     .replace('GTI_ADD_SC', str(args.gti_add_sc))\
@@ -710,7 +710,7 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
             for n, (tempi, temp0) in enumerate(zip(args.heat_temps[:-1], args.heat_temps[1:]), 1):
                 comp_md_steps['heat-%s'%str(n)] = COMPLEX_RESTRAINT_HEAT\
                     .replace('CLAMBDA', str(_lambda))\
-                    .replace('DT', str(args.timestep))\
+                    .replace('DT', str(0.002))\
                     .replace('CUT', str(args.cutoff))\
                     .replace('TEMPI', str(tempi))\
                     .replace('TEMP0', str(temp0))\
@@ -720,7 +720,7 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
                     .replace('RESTRAINTMASK', str(args.restraintmask))
                 comp_md_steps['press-%s'%str(n)] = COMPLEX_RESTRAINT_PRESS\
                     .replace('CLAMBDA', str(_lambda))\
-                    .replace('DT', str(args.timestep))\
+                    .replace('DT', str(0.002))\
                     .replace('CUT', str(args.cutoff))\
                     .replace('TEMP0', str(temp0))\
                     .replace('GTI_ADD_SC', str(args.gti_add_sc))\

diff --git a/abfe/abfe_equilibration.py b/abfe/abfe_equilibration.py
@@ -118,15 +118,15 @@ def _parse_args():
         .replace('CUT', str(args.cutoff))
     for n, (tempi, temp0) in enumerate(zip(args.heat_temps[:-1], args.heat_temps[1:]), 1):
         lig_equil_steps['heat-%s'%str(n)] = SOLVATED_HEAT\
-            .replace('DT', str(args.timestep))\
+            .replace('DT', str(0.002))\
             .replace('CUT', str(args.cutoff))\
             .replace('TEMPI', str(tempi))\
             .replace('TEMP0', str(temp0))\
             .replace('TEMP_0', 'TEMP0')\
             .replace('RESTRAINT_WT', str(args.restraint_wt))\
             .replace('RESTRAINTMASK', str(args.restraintmask))
         lig_equil_steps['press-%s'%str(n)] = SOLVATED_PRESS\
-            .replace('DT', str(args.timestep))\
+            .replace('DT', str(0.002))\
             .replace('CUT', str(args.cutoff))\
             .replace('TEMP0', str(temp0))\
             .replace('RESTRAINT_WT', str(args.restraint_wt))\
@@ -188,15 +188,15 @@ def _parse_args():
             .replace('CUT', str(args.cutoff))
         for n, (tempi, temp0) in enumerate(zip(args.heat_temps[:-1], args.heat_temps[1:]), 1):
             comp_equil_steps['heat-%s'%str(n)] = COMPLEX_HEAT\
-                .replace('DT', str(args.timestep))\
+                .replace('DT', str(0.002))\
                 .replace('CUT', str(args.cutoff))\
                 .replace('TEMPI', str(tempi))\
                 .replace('TEMP0', str(temp0))\
                 .replace('TEMP_0', 'TEMP0')\
                 .replace('RESTRAINT_WT', str(args.restraint_wt))\
                 .replace('RESTRAINTMASK', str(args.restraintmask))
             comp_equil_steps['press-%s'%str(n)] = COMPLEX_PRESS\
-                .replace('DT', str(args.timestep))\
+                .replace('DT', str(0.002))\
                 .replace('CUT', str(args.cutoff))\
                 .replace('TEMP0', str(temp0))\
                 .replace('RESTRAINT_WT', str(args.restraint_wt))\