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gmx-convert-tpr(1)		GROMACS Manual		    gmx-convert-tpr(1)

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

SYNOPSIS
       gmx convert-tpr [-s [<.tpr/.tpb/...>]] [-f [<.trr/.cpt/...>]]
		    [-e [<.edr>]] [-n [<.ndx>]] [-o [<.tpr/.tpb/...>]]
		    [-nice <int>] [-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 This option is obsolete, since  mdrun  now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 contin‐
       uation 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. WARN‐
       ING: 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 and output files:

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
	   Run input file: tpr tpb tpa

       -f [<.trr/.cpt/...>] (traj.trr) (Input, Optional)
	   Full precision trajectory: trr cpt trj tng

       -e [<.edr>] (ener.edr) (Input, Optional)
	   Energy file

       -n [<.ndx>] (index.ndx) (Input, Optional)
	   Index file

       -o [<.tpr/.tpb/...>] (tpxout.tpr) (Output)
	   Run input file: tpr tpb tpa

       Other options:

       -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]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
       gromacs(7)

       More   information  about  GROMACS  is  available  at  <http://www.gro‐
       macs.org/>.

VERSION 5.0.6						    gmx-convert-tpr(1)

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