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 This option is obsolete, since mdrun now writes and reads checkpoint files.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