simulation.physical_validation submodule

cg_openmm.simulation.physical_validation.physical_validation_ensemble(output_data='output.nc', output_directory='ouput', plotfile='ensemble_check', pairs='single', ref_state_index=0)

Run ensemble physical validation test for 2 states in replica exchange simulation

Parameters

• output_data (str) – Path to the output data for a NetCDF-formatted file containing replica exchange simulation data

• plotfile (str) – Filename for outputting ensemble check plot

• pairs – Option for running ensemble validation on all replica pair combinations (‘all’), adjacent pairs (‘adjacent’), or single pair with optimal spacing (‘single’)

• ref_state_index (int) – Index in temperature_list to use as one of the states in the ensemble check. The other state will be chosen based on the energy standard deviation at the reference state. Ignored if pairs=’all’

cg_openmm.simulation.physical_validation.set_simulation_data(state_energies, T_array, state1_index, state2_index)

Create and set SimulationData objects for a pair of specified states