NAME

       tpbconv - makes a run input file for restarting a crashed run

       VERSION 4.6.5

SYNOPSIS

       tpbconv  -s  topol.tpr  -f  traj.trr -e ener.edr -n index.ndx -o tpxout.tpr -[no]h -[no]version -nice int
       -extend real -until real -nsteps int -time real -[no]zeroq -[no]vel -[no]cont -init_fep_state int

DESCRIPTION

       tpbconv 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  This option is obsolete,  since  mdrun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.

FILES

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -f traj.trr Input, Opt.
        Full precision trajectory: trr trj cpt

       -e ener.edr Input, Opt.
        Energy file

       -n index.ndx Input, Opt.
        Index file

       -o tpxout.tpr Output
        Run input file: tpr tpb tpa

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 0
        Set the nicelevel

       -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]zeroqno
        Set the charges of a group (from the index) to zero

       -[no]velyes
        Require velocities from trajectory

       -[no]contyes
        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

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                       tpbconv(1)