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tpbconvMain Table of Contents |
VERSION 4.6.3
Fri 5 Jul 2013
| VERSION 4.6.3 |
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 This option is obsolete, since mdrun now writes and reads checkpoint files.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.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[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 |