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gmx-convert-tpr(1)              GROMACS Manual              gmx-convert-tpr(1)

NAME

gmx-convert-tpr - Make a modifed run-input file

SYNOPSIS

gmx convert-tpr [-s [<.tpr/.tpb/...>]] [-f [<.trr/.cpt/...>]] [-e [<.edr>]] [-n [<.ndx>]] [-o [<.tpr/.tpb/...>]] [-nice <int>] [-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 This option is obsolete, since mdrun now writes and reads checkpoint files.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 and output files: -s [<.tpr/.tpb/...>] (topol.tpr) (Input) Run input file: tpr tpb tpa -f [<.trr/.cpt/...>] (traj.trr) (Input, Optional) Full precision trajectory: trr cpt trj tng -e [<.edr>] (ener.edr) (Input, Optional) Energy file -n [<.ndx>] (index.ndx) (Input, Optional) Index file -o [<.tpr/.tpb/...>] (tpxout.tpr) (Output) Run input file: tpr tpb tpa Other options: -nice <int> (0) Set the nicelevel -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

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. VERSION 5.0.6 gmx-convert-tpr(1)

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