cg_openmm.parameters.reweight

Functions

bin_samples(sample_kn, n_bins)
get_decorrelated_samples(replica_positions, ...)	Given a set of replica exchange trajectories, energies, and associated temperatures, this function returns decorrelated samples, as obtained from pymbar with timeseries.subsampleCorrelatedData.
get_enthalpy_differences(mbar)	Given an MBAR class object, this function computes the enthalpy differences for the states defined within.
get_entropy_differences(mbar)	Given an MBAR class object, this function computes the entropy differences for the states defined within.
get_free_energy_differences(mbar)	Given an MBAR class object, this function computes the free energy differences for the states defined within.
get_intermediate_temperatures(T_from_file, ...)	Given a list of temperatures and a number of intermediate states as input, this function calculates the values for temperatures intermediate between those in this list, as the mean between values in the list.
get_mbar_expectation(E_kln, ...[, output, mbar])	Given a properly-formatted matrix of energies with associated temperatures this function reweights with MBAR (if 'mbar'=None), and can also compute the expectation value for any property of interest.
get_opt_temperature_list(...[, ...])	Given an initial temperature list, and heat capacity curve that resulted from a replica exchange simulation using those temperatures, computes a revised temperature list satisfying the constant entropy increase (CEI) method
get_temperature_list(min_temp, max_temp, ...)	Given the parameters to define a temperature range as input, this function uses logarithmic spacing to generate a list of intermediate temperatures.