diff --git a/abfe/abfe_alchemy_md.py b/abfe/abfe_alchemy_md.py index 77890d5..b47676b 100644 --- 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 index bea622e..b8691c5 100644 --- a/abfe/abfe_equilibration.py +++ b/abfe/abfe_equilibration.py @@ -118,7 +118,7 @@ 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))\ @@ -126,7 +126,7 @@ def _parse_args(): .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))\ @@ -188,7 +188,7 @@ 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))\ @@ -196,7 +196,7 @@ def _parse_args(): .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))\