xenial (1) gmx-convert-tpr.1.gz

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  This option is obsolete, since mdrun now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)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2015, GROMACS development team