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 This option is obsolete, since mdrun now writes and reads checkpoint files.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