NAME
tpbconv - makes a run input file for restarting a crashed run
VERSION 4.0.1
SYNOPSIS
tpbconv -s topol.tpr -f traj.trr -e ener.edr -n index.ndx -o tpxout.tpr
-[no]h -nice int -nsteps int -runtime real -time real -extend real
-until real -[no]zeroq -[no]cont
DESCRIPTION
tpbconv can edit run input files in four ways.
1st. by modifying the number of steps in a run input file with option
-nsteps or option -runtime.
2st. (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 This option is obsolete, since mdrun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.
3nd. 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 Ca tpx file. WARNING: this tpx
file is not fully functional. 4rd. 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: edr ene
-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
-nice int 0
Set the nicelevel
-nsteps int -1
Change the number of steps
-runtime real -1
Set the run time (ps)
-time real -1
Continue from frame at this time (ps) instead of the last frame
-extend real 0
Extend runtime by this amount (ps)
-until real 0
Extend runtime until this ending time (ps)
-[no]zeroqno
Set the charges of a group (from the index) to zero
-[no]contyes
For exact continuation, the constraints should not be solved before
the first step
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 tpbconv(1)