8000 Allow override t0 and g_t when computing free energy by zhang-ivy · Pull Request #585 · choderalab/openmmtools · GitHub
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Allow override t0 and g_t when computing free energy #585

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Allow override t0 and g_t when computing free energy #585

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11 changes: 10 additions & 1 deletion openmmtools/multistate/multistateanalyzer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1442,11 +1442,18 @@ def get_effective_energy_timeseries(self, energies=None, neighborhoods=None, rep
logger.debug("Done.")
return u_n

def _compute_mbar_decorrelated_energies(self):
def _compute_mbar_decorrelated_energies(self, t0=None, subsample_rate=None):
"""Return an MBAR-ready decorrelated energy matrix.

The data is returned after discarding equilibration and truncating
the iterations to self.max_n_iterations.

Parameters
----------
t0 : int, optional
the number of equilibrated iterations to override number_equilibrated
subsample_rate : int, optional
the subsample rate to override g_t

Returns
-------
Expand All @@ -1464,6 +1471,8 @@ def _compute_mbar_decorrelated_energies(self):
# Use the cached information to generate the equilibration data.
sampled_energy_matrix, unsampled_energy_matrix, neighborhoods, replicas_state_indices = energy_data
number_equilibrated, g_t, Neff_max = self._get_equilibration_data(sampled_energy_matrix, neighborhoods, replicas_state_indices)
number_equilibrated = t0 if t0 is not None else number_equilibrated
g_t = subsample_rate if subsample_rate is not None else g_t

logger.debug("Assembling uncorrelated energies...")

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