gmx convert-tpr#

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