gmx convert-tpr

Synopsis

gmx convert-tpr [-s [<.tpr>]] [-f [<.trr/.cpt/...>]] [-e [<.edr>]]
             [-n [<.ndx>]] [-o [<.tpr>]] [-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 This option is obsolete, since mdrun now writes and reads checkpoint files.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 files:

-s [<.tpr>] (topol.tpr)

Portable xdr run input file

-f [<.trr/.cpt/…>] (traj.trr) (Optional)

Full precision trajectory: trr cpt tng

-e [<.edr>] (ener.edr) (Optional)

Energy file

-n [<.ndx>] (index.ndx) (Optional)

Index file

Options to specify output files:

-o [<.tpr>] (tprout.tpr)

Portable xdr run input file

Other options:

-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