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:

-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

SEE ALSO

gmx(1)

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