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Man Pages


Manual Reference Pages  -  GMX-CONVERT-TPR (1)

NAME

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

CONTENTS

Synopsis
Description
Options
See Also

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 This option is obsolete, since mdrun now writes and reads checkpoint files.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/>.

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VERSION 5.0.6 GMX-CONVERT-TPR (1)

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