Title: Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

Abstract

Here, we compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium.

Authors:

Lincoff, James  ^[1];

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Sasmal, Sukanya ^[1]; Head-Gordon, Teresa ^[2]

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+ Show Author Affiliations

1. Univ. of California, Berkeley, CA (United States)
2. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Publication Date:

Thu Nov 03 00:00:00 EDT 2016

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

OSTI Identifier:

1413710

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Accepted Manuscript

Journal Name:

Journal of Chemical Physics

Additional Journal Information:

Journal Volume: 145; Journal Issue: 17; Journal ID: ISSN 0021-9606

Publisher:

American Institute of Physics (AIP)

Country of Publication:

United States

Language:

English

Subject:

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY