schrodinger.application.desmond.msj_generator.lambda_dynamics module

class schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator(jobname: str, cd_params: Dict[str, object], pmf_coefficients_fname: Optional[str] = None, mutations_filename: str = 'mutations.txt', **kwargs)

Bases: schrodinger.application.desmond.mapper_msj_generator.BaseFepMsjGenerator

Msj generator class for the Lambda Dynamics workflow.

This class generates a main job msj from the template lambda_dynamics.msj and sets the user-supplied mutations_filename option in the LambdaDynamicsMapper stage and sets the job command and pmf_coefficients option for the LambdaDynamicsMdLauncher stage. This class also generates a md subjob msj from the lambda_dynamics_md.msj.

TEMPLATE_MSJ = 'lambda_dynamics.msj'
TEMPLATE_MD_MSJ = 'lambda_dynamics_md.msj'
TEMPLATE_CFG = 'lambda_dynamics.cfg'
__init__(jobname: str, cd_params: Dict[str, object], pmf_coefficients_fname: Optional[str] = None, mutations_filename: str = 'mutations.txt', **kwargs)

# TODO consider renaming cpus to gpus or more generic slots :param jobname: The jobname.

Parameters

  • cd_params – A dictionary with cpus set to the number of gpu slots to use, and ‘mps_factor` set to the number of processes per GPU.

  • forcefield (str) – The name of the forcefield to use.

  • sim_time (int) – The simulation time for the production stage in ps.

  • sim_time_complex (int) – The simulation time for the complex leg in ps

  • sim_time_solvent (int) – The simulation time for the solvent leg in ps

  • rand_seed (int) – The random seed.

  • ensemble (str) – The ensemble, NPT or NVT.

  • buffer_width (float) – The buffer width in Angstrom determines how much solvent is added to the solute. This is only used if it is larger than the default buffer width.

  • lambda_windows (int) – Number of lambda replicas to use for the FEP stages.

  • custom_charge_mode (CUSTOM_CHARGE_MODE) – Set to CUSTOM_CHARGE_MODE.ASSIGN to assign custom charges. Set to CUSTOM_CHARGE_MODE.CLEAR to clear custom charges if present, without reassigning. Set to CUSTOM_CHARGE_MODE.KEEP to keep existing custom charges if present.

  • h_mass (bool) – Set to True to enable hydrogen mass repartitioning and False to disable it. Default is True.

  • concatenate (bool) – Set to True to concatenate the equilibration FEP stages. Default is True.

  • max_walltime – Maximum walltime in seconds before the subjobs are automatically checkpointed and restarted. The default of 0 means to not set a maximum walltime.

write_main_msj() → str

Write the main msj for the workflow.

write_md_msj() → str

Write the md msj for the workflow.

write_cfg() → str

Write the cfg used for md simulations in the workflow.

generate_msj() → List[schrodinger.utils.sea.sea.Map]

Generate the main msj for the workflow.

generate_md_msj() → List[schrodinger.utils.sea.sea.Map]

Generate the md msj for the workflow.

generate_cfg() → schrodinger.utils.sea.sea.Map