Main Table of Contents

Fri 5 Jul 2013


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 This option is obsolete, since mdrun now writes and reads checkpoint files.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


-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]h bool no Print help info and quit
-[no]version bool no 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]zeroq bool no Set the charges of a group (from the index) to zero
-[no]vel bool yes Require velocities from trajectory
-[no]cont bool yes For exact continuation, the constraints should not be applied before the first step
-init_fep_state int 0 fep state to initialize from