NAME¶

tpbconv - makes a run input file for restarting a crashed run VERSION 4.5.4-dev-20110404-bc5695c

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

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 This option is obsolete, since mdrun now writes and reads checkpoint files.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

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.