BioSimSpace.MD.run¶
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BioSimSpace.MD.run(system, protocol, engine='auto', gpu_support=False, auto_start=True, name='md', work_dir=None, seed=None, property_map={}, ignore_warnings=False, show_errors=True)¶ Auto-configure and run a molecular dynamics process.
- Parameters
system (
System) – The molecular system.protocol (
Protocol) – The simulation protocol.engine (str) – The molecular dynamics engine to use. If “auto”, then a matching engine will automatically be chosen. Supported engines can be found using ‘BioSimSpace.MD.engines()’.
gpu_support (bool) – Whether to choose an engine with GPU support.
auto_start (bool) – Whether to start the process automatically.
name (str) – The name of the process.
work_dir (str) – The working directory for the process.
seed (int) – A random number seed.
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
ignore_warnings (bool) – Whether to ignore warnings when generating the binary run file. This option is specific to GROMACS and will be ignored when a different molecular dynamics engine is chosen.
show_errors (bool) – Whether to show warning/error messages when generating the binary run file. This option is specific to GROMACS and will be ignored when a different molecular dynamics engine is chosen.
- Returns
process – A process to run the molecular dynamics protocol.
- Return type