Expanded ensemble #421
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Expanded ensemble #421
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ajsilveira
commented
May 10, 2019
ajsilveira
commented
- Include the option weight_update to perform expanded ensemble simulations
- minimum_visits and beta_factor are defined by the user
- set histogram as the default for flatness criteria
andrrizzi
reviewed
May 14, 2019
| @@ -628,7 +648,6 @@ def _update_logZ_estimates(self, replicas_log_P_k): | |||
| for (replica_index, state_index) in enumerate(self._replica_thermodynamic_states): | |||
| logger.debug(' Replica %d state %d' % (replica_index, state_index)) | |||
| # Compute attenuation factor gamma | |||
| beta_factor = 0.8 | |||
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This may be the main cause of test errors. The local variable beta_factor is deleted here, but I don't see self.beta_factor used anywhere.
Update everything to match MolSSI cookiecutter
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Thank you! I think this is ready to be merged. Can you just update the |
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This would be an "enhancement" in 0.19.0 version ? |
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Yes, that works. |
Another small fix to release notes
Fix restrained atom indices
Co-Authored-By: Josh Fass <josh.fass@choderalab.org>
…m/choderalab/openmmtools into loopy_alchemical_customintegrator
Fix travis since miniconda changed location
…ors from @domrufa)
…rium-integrator Add PeriodicNonequilibriumIntegrator
…ilibrium periodic integration cycle
…ilibrium Fix an issue with accidentally resetting PeriodicNonequilibriumIntegrator
Update neq integrator tests to generate trajectory.
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