GMX-CONVERT-TPR(1) | GROMACS | GMX-CONVERT-TPR(1) |
NAME¶
gmx-convert-tpr - Make a modifed run-input fileSYNOPSIS¶
gmx convert-tpr [-s [<.tpr>]] [-f [<.trr/.cpt/...>]] [-e [<.edr>]] [-n [<.ndx>]] [-o [<.tpr>]] [-extend <real>] [-until <real>] [-nsteps <int>] [-time <real>] [-[no]zeroq] [-[no]vel] [-[no]cont] [-init_fep_state <int>]
DESCRIPTION¶
gmx convert-tpr can edit run input files in four 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. (OBSOLETE) by creating a run input file for a continuation run when your simulation has crashed due to e.g. a full disk, or by making a continuation run input file. This option is obsolete, since mdrun now writes and reads checkpoint files. Note that a frame with coordinates and velocities is needed. When pressure and/or Nose-Hoover temperature coupling is used an energy file can be supplied to get an exact continuation of the original run.
3. 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.
4. 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>] (topol.tpr)
- Portable xdr run input file
- -f [<.trr/.cpt/...>] (traj.trr) (Optional)
- Full precision trajectory: trr cpt tng
- -e [<.edr>] (ener.edr) (Optional)
- Energy file
- -n [<.ndx>] (index.ndx) (Optional)
- Index file
Options to specify output files:
- -o [<.tpr>] (tprout.tpr)
- Portable xdr run input file
Other options:
- -extend <real> (0)
- Extend runtime by this amount (ps)
- -until <real> (0)
- Extend runtime until this ending time (ps)
- -nsteps <int> (0)
- Change the number of steps
- -time <real> (-1)
- Continue from frame at this time (ps) instead of the last frame
- -[no]zeroq (no)
- Set the charges of a group (from the index) to zero
- -[no]vel (yes)
- Require velocities from trajectory
- -[no]cont (yes)
- For exact continuation, the constraints should not be applied before the first step
- -init_fep_state <int> (0)
- fep state to initialize from
SEE ALSO¶
gmx(1)More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2016, GROMACS development teamOctober 28, 2016 | 2016.1 |