Provided by: gromacs-data_4.6.5-1build1_all bug


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

       VERSION 4.6.5


       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


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       option is obsolete, since mdrun now writes and reads checkpoint files.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


       -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


        Print help info and quit

        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

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

        Require velocities from trajectory

        For exact continuation, the constraints should not be applied before the first step

       -init_fep_state int 0
        fep state to initialize from



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               tpbconv(1)