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g_tpbconv
Langue: en
Version: 371270 (fedora - 01/12/10)
Section: 1 (Commandes utilisateur)
NAME
tpbconv - makes a run input file for restarting a crashed runVERSION 4.5
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]contDESCRIPTION
tpbconv can edit run input files in four ways.1st. by modifying the number of steps in a run input file with options -extend, -until or -nsteps (nsteps=-1 means unlimited number of steps)
2nd. (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 This option is obsolete, since mdrun now writes and reads checkpoint files.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.
3rd. 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. 4th. 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 InputRun 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]hnoPrint 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/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre