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tpbconvMain Table of Contents |
VERSION 3.2.0
Sun 25 Jan 2004
| VERSION 3.2.0 |
tpbconv can edit run input files in three ways.
1st. 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. Note that a frame with coordinates and velocities is needed, which means that when you never write velocities, you can not use tpbconv and you have to start the run again from the beginning. When pressure and/or temperature coupling is used an energy file can be supplied to get an exact continuation of the original run.
2nd. 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. 3rd. by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interactio Energy) method.
| option | filename | type | description |
|---|---|---|---|
| -s | topol.tpr | Input | Generic run input: tpr tpb tpa xml |
| -f | traj.trr | Input, Opt. | Full precision trajectory: trr trj |
| -e | ener.edr | Input, Opt. | Generic energy: edr ene |
| -n | index.ndx | Input, Opt. | Index file |
| -o | tpxout.tpr | Output | Generic run input: tpr tpb tpa xml |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 0 | Set the nicelevel |
| -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]zeroq | bool | no | Set the charges of a group (from the index) to zero |
| -[no]unconstrained | bool | yes | For a continuous trajectory, the constraints should not be solved before the first step (default) |