PROPERTY EVALUATOR FREE FULL

SolvationYankProtocol ( 'run_solvation_yank' ) run_yank. coordinate_file_path = ProtocolPath ( 'coordinate_file_path', build_vacuum_coordinates. substance = ProtocolPath ( 'filtered_substance', filter_solute. force_field_path = ProtocolPath ( 'force_field_path', 'global' ) assign_vacuum_parameters. BaseBuildSystem ( 'assign_parameters' ) assign_vacuum_parameters. max_molecules = 1 assign_vacuum_parameters = forcefield. BuildCoordinatesPackmol ( 'build_vacuum_coordinates' ) build_vacuum_coordinates. component_roles = # Setup the solute in vacuum system. input_substance = ProtocolPath ( 'substance', 'global' ) filter_solute. FilterSubstanceByRole ( 'filter_solute' ) filter_solute. component_roles = filter_solute = miscellaneous. input_substance = ProtocolPath ( 'substance', 'global' ) filter_solvent. FilterSubstanceByRole ( 'filter_solvent' ) filter_solvent. id ) # Create a substance which only contains the solute (e.g. input_coordinate_file = ProtocolPath ( 'output_coordinate_file', energy_minimisation. parameterized_system = ProtocolPath ( 'parameterized_system', assign_full_parameters. thermodynamic_state = ProtocolPath ( 'thermodynamic_state', 'global' ) equilibration_simulation. output_frequency = 10000 equilibration_simulation. steps_per_iteration = 100000 equilibration_simulation.

OpenMMSimulation ( 'equilibration_simulation' ) equilibration_simulation. input_coordinate_file = ProtocolPath ( 'coordinate_file_path', build_full_coordinates. OpenMMEnergyMinimisation ( 'energy_minimisation' ) energy_minimisation.

PROPERTY EVALUATOR FREE FULL

id ) # Perform a quick minimisation of the full system to give # YANK a better starting point for its minimisation. coordinate_file_path = ProtocolPath ( 'coordinate_file_path', build_full_coordinates. substance = ProtocolPath ( 'substance', 'global' ) assign_full_parameters. force_field_path = ProtocolPath ( 'force_field_path', 'global' ) assign_full_parameters. BaseBuildSystem ( 'assign_solvated_parameters' ) assign_full_parameters. max_molecules = n_molecules assign_full_parameters = forcefield. substance = ProtocolPath ( 'substance', 'global' ) build_full_coordinates. BuildCoordinatesPackmol ( 'build_solvated_coordinates' ) build_full_coordinates. relative_tolerance = relative_tolerance use_target_uncertainty = ( absolute_tolerance != UNDEFINED or relative_tolerance != UNDEFINED ) # Setup the fully solvated systems. absolute_tolerance = absolute_tolerance calculation_schema.

''' assert absolute_tolerance = UNDEFINED or relative_tolerance = UNDEFINED calculation_schema = SimulationSchema () calculation_schema. Returns - SimulationSchema The schema to follow when estimating this property. n_molecules: int The number of molecules to use in the simulation. relative_tolerance: float The tolerance (as a fraction of the properties reported uncertainty) to estimate the property to within. Parameters - absolute_tolerance:, optional The absolute tolerance to estimate the property to within. Def default_simulation_schema ( absolute_tolerance = UNDEFINED, relative_tolerance = UNDEFINED, n_molecules = 2000 ): '''Returns the default calculation schema to use when estimating this class of property from direct simulations.

Property evaluator free