Command line tool: driver
| Module | cltools |
|---|---|
| Description | Input |
| analyze trajectories with plumed | command line args |
Details
Text from manual goes here
Syntax
The following table describes the command line options that are available for this tool
| Keyword | Description |
|---|---|
| --help/-h | print this help |
| --help-debug | print special options that can be used to create regtests |
| --plumed | specify the name of the plumed input file |
| --timestep | the timestep that was used in the calculation that produced this trajectory in picoseconds |
| --trajectory-stride | the frequency with which frames were output to this trajectory during the simulation (0 means that the number of the step is read from the trajectory file, currently working only for xtc/trr files read with --ixtc/--trr) |
| --multi | set number of replicas for multi environment (needs MPI) |
| --noatoms | don't read in a trajectory |
| --parse-only | read the plumed input file and stop |
| --restart | makes driver behave as if restarting |
| --ixyz | the trajectory in xyz format |
| --igro | the trajectory in gro format |
| --idlp4 | the trajectory in DL_POLY_4 format |
| --ixtc | the trajectory in xtc format (xdrfile implementation) |
| --itrr | the trajectory in trr format (xdrfile implementation) |
| --shortcut-ofile | the name of the file to output info on the way shortcuts have been expanded |
| --valuedict-ofile | output a dictionary giving information about each value in the input file |
| --length-units | units for length, either as a string or a number |
| --mass-units | units for mass in pdb and mc file, either as a string or a number |
| --charge-units | units for charge in pdb and mc file, either as a string or a number |
| --kt | set kT it will not be necessary to specify temperature in input file |
| --dump-forces | dump the forces on a file |
| --dump-forces-fmt | the format to use to dump the forces |
| --dump-full-virial | with --dump-forces, it dumps the 9 components of the virial |
| --pdb | provides a pdb with masses and charges |
| --mc | provides a file with masses and charges as produced with DUMPMASSCHARGE |
| --box | comma-separated box dimensions (3 for orthorhombic, 9 for generic) |
| --natoms | provides number of atoms - only used if file format does not contain number of atoms |
| --initial-step | provides a number for the initial step, default is 0 |
| --debug-forces | output a file containing the forces due to the bias evaluated using numerical derivatives and using the analytical derivatives implemented in plumed |
| --debug-float | [yes/no] turns on the single precision version (to check float interface) |
| --debug-dd | [yes/no] use a fake domain decomposition |
| --debug-pd | [yes/no] use a fake particle decomposition |
| --debug-grex | use a fake gromacs-like replica exchange, specify exchange stride |
| --debug-grex-log | log file for debug=grex |
| --mf_dcd | molfile: the trajectory in dcd format |
| --mf_crd | molfile: the trajectory in crd format |
| --mf_crdbox | molfile: the trajectory in crdbox format |
| --mf_gro | molfile: the trajectory in gro format |
| --mf_g96 | molfile: the trajectory in g96 format |
| --mf_trr | molfile: the trajectory in trr format |
| --mf_trj | molfile: the trajectory in trj format |
| --mf_xtc | molfile: the trajectory in xtc format |
| --mf_pdb | molfile: the trajectory in pdb format |