gmx-convert-tpr1
Make a modified run-input file
Usage
gmx convert-tpr [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-o [<.tpr/.gro/...>]] [-extend <time>] [-until <time>]
[-nsteps <int>] [-[no]generate_velocities]
[-velocity_temp <real>] [-velocity_seed <int>]
Overview
gmx convert-tpr can edit run input files in three ways.
1. by modifying the number of steps in a run input file with options -extend, -until or -nsteps (nsteps=-1 means unlimited number of steps)
2. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional.
3. by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method.
Options
Options to specify input files:
-s [<.tpr/.gro/...>] (topol.tpr)
|
Run input file to modify: tpr gro g96 pdb brk ent |
|---|---|
-n [<.ndx>] (index.ndx) (Optional)
|
File containing additional index groups |
Options to specify output files:
- -o [<.tpr/.gro/...>] (tprout.tpr) (Optional)
-
Generated modified run input file: tpr gro g96 pdb brk ent
Other options:
-extend <time> (0)
|
Extend runtime by this amount (ps) |
|---|---|
-until <time> (0)
|
Extend runtime until this ending time (ps) |
-nsteps <int> (0)
|
Change the number of steps remaining to be made |
-[no]generate_velocities (no)
|
Reassign velocities, using a generated seed unless one is explicitly set |
-velocity_temp <real> (300)
|
Temperature to use when generating velocities |
-velocity_seed <int> (-1)
|
Random seed for velocities. If value is -1, a new one is generated |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.