BioSimSpace.MD.run

BioSimSpace.MD.run(system, protocol, 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.

  • gpu_support (bool) – Whether to choose a package 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

Process