NAME

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

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       is obsolete, since mdrun now writes and reads checkpoint files.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

SEE ALSO

       gmx(1)

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COPYRIGHT

       2015, GROMACS development team