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, frame_start=0, frame_stride=1, frame_end=-1, bootstrap_error=False, bootstrap_repetitions=200, bootstrap_seed=None, data_is_uncorrelated=False)[source]
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’
frame_start (int) – Set the starting frame for the analysis (default=0)
frame_stride (int) – Set the sample spacing for decorrelated frames (default=1)
frame_end (int) – Set the end frame for the analysis (default=-1)
bootstrap_error (bool) – Flag indicating if standard error of energies should be computed via bootstrapping (default=False)
bootstrap_repetitions (int) – Number of bootstrap repititions (default=200)
bootstrap_seed (int) – Set a bootstrapping seed for reproducible results. If None, a random seed is used. (default=None)
data_is_uncorrelated (bool) – Flag indicating if the data after applying frame_start, frame_stride, and frame_end is uncorrelated. Applying the appropriate frame slicing greatly speeds up the ensemble check. (default=False)