BioSimSpace.MD.run

BioSimSpace.MD.run(system, protocol, autostart=True, name='md', work_dir=None, seed=None, property_map={})

Auto-configure and run a molecular dynamics process.

Parameters:
  • system (System) – The molecular system.
  • protocol (Protocol) – The simulation protocol.
  • autostart (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” }
Returns:

process – A process to run the molecular dynamics protocol.

Return type:

Process