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GMX-CONVERT-TPR(1) GROMACS GMX-CONVERT-TPR(1)

NAME

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

SYNOPSIS

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>]


DESCRIPTION

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:

Run input file to modify: tpr gro g96 pdb brk ent
File containing additional index groups

Options to specify output files:

Generated modified run input file: tpr gro g96 pdb brk ent

Other options:

Extend runtime by this amount (ps)
Extend runtime until this ending time (ps)
Change the number of steps remaining to be made
-[no]generate_velocities (no)
Reassign velocities, using a generated seed unless one is explicitly set
Temperature to use when generating velocities
Random seed for velocities. If value is -1, a new one is generated

SEE ALSO

gmx(1)

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COPYRIGHT

2024, GROMACS development team

November 18, 2024 2025.0-beta