, protocol, engine='auto', gpu_support=False, auto_start=True, name='md', work_dir=None, seed=None, property_map={}, **kwargs)[source]#

Auto-configure and run a molecular dynamics process.

  • 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” }

  • kwargs (dict) – A dictionary of optional keyword arguments neeeded by the engine.


process – A process to run the molecular dynamics protocol.

Return type: