Molecular dynamics parameters¶
General information¶
The entry script for ChemLab is in src/start_simulation.py which provides a number of command-line options. The complete list can be found here: start_simulation.py.
All options described here can be either passed by –<option_name> in the command-line or placed in the params file. The parameters from params file can be loaded by:
$ python src/start_simulation.py @params
General options¶
- conf
- Input coordinate file. Currently only .gro file format is supported.
- topol
- Input topology file. This is a GROMACS-like file format. See: Topology file format.
- node_grid
- If provided then use a custom node grid, format: node_x,node_y,node_z.
- skin
- The parameter for Verlet list algorithm.
- output_prefix
- Add prefix to all output files.
- trj_collect
- Collect trajectory every n-steps.
- energy_collect
- Collect system information like potential energy, temperature and others every n-steps.
- topol_collect
- Collect topology information every n-steps. The information are stored in HDF5 file along with trajectory information.
- reactions
- The reaction settings file.
- exclusion_list
- The file with the list of particle pairs to be excluded from non-bonded interactions.
- max_force
- The maximum value of the force in the system. If the force computed on any particle is larger than this value then the max_force is used (preserving the direction of force vector).
Running¶
- run
- The number of simulation steps to run
- start_ar
- The simulation step when the chemical reactions are enabled
- stop_ar
- The simulation step when the chemical reactions are disabled
- rng_seed
- The seed for random number generator.
- gen_velocity
- Generate velocities according to Maxwell-Boltzmann distribution