Try a fast=False in detectEquilibration
@@ -141,7 +141,7 @@ def subtest_mcmc_expectation(testsystem, move):
testsystem.__class__.__name__)
potential_expectation = testsystem.get_potential_expectation(thermodynamic_state) / kT
- [t0, g, Neff_max] = timeseries.detectEquilibration(potential_n)
+ [t0, g, Neff_max] = timeseries.detectEquilibration(potential_n, fast=False)
potential_mean = potential_n[t0:].mean()
dpotential_mean = potential_n[t0:].std() / Neff_max
potential_error = potential_mean - potential_expectation
@@ -164,7 +164,7 @@ def subtest_mcmc_expectation(testsystem, move):
testsystem.__class__.__name__)
volume_expectation = testsystem.get_volume_expectation(thermodynamic_state) / (unit.nanometers**3)
- [t0, g, Neff_max] = timeseries.detectEquilibration(volume_n)
+ [t0, g, Neff_max] = timeseries.detectEquilibration(volume_n, fast=False)
volume_mean = volume_n[t0:].mean()
dvolume_mean = volume_n[t0:].std() / Neff_max
volume_error = volume_mean - volume_expectation
