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Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing
John D Chodera1, Michael R Shirts
1California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, 260J Stanley Hall, Berkeley, California 94720, USA. jchodera@berkeley.edu
The Journal of Chemical Physics
|November 25, 2011
Summary
This study reframes replica exchange and expanded ensemble algorithms as Gibbs sampling. Novel state index updating strategies improve phase space mixing for enhanced molecular simulations.
Area of Science:
- Molecular dynamics and biophysics
- Computational chemistry
- Statistical inference
Background:
- Replica exchange and expanded ensemble algorithms are popular for molecular simulations.
- Enhancing phase space mixing is crucial for efficient sampling of molecular configurations.
- Current methods can lead to suboptimal mixing and longer simulation times.
Purpose of the Study:
- To demonstrate that replica exchange and expanded ensemble algorithms are special cases of Gibbs sampling.
- To introduce improved methods for updating thermodynamic state indices to enhance Markov chain mixing.
- To reduce simulation times for obtaining precise estimates in molecular simulations.
Main Methods:
- Framing replica exchange and expanded ensemble as Gibbs sampling within a Markov chain Monte Carlo framework.
- Developing and applying novel strategies for updating thermodynamic state indices.
- Testing improved schemes on alchemical expanded ensemble, parallel tempering, and multidimensional replica exchange umbrella sampling.
Main Results:
- Judicious updating of thermodynamic state indices significantly increases Markov chain mixing.
- Proposed simple, inexpensive alternatives to common state update methods improve mixing.
- Reduced simulation times were observed for obtaining estimates of desired precision.
Conclusions:
- Gibbs sampling provides a unifying framework for understanding and improving popular molecular simulation protocols.
- Enhanced state index updating strategies offer a practical way to boost the efficiency of complex molecular simulations.
- The developed methods are broadly applicable to various enhanced sampling techniques in chemistry and biophysics.
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