g_tpbconv_d (1) - Linux Manuals

g_tpbconv_d: makes a run input file for restarting a crashed run

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 This option is obsolete, since mdrun now writes and reads checkpoint files.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