Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 6, Issue 9, Pages 2804-2808Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct100281c
Keywords
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Funding
- University of Florida High-Performance Computing Center
- NSF Large Allocations Resource Committee [TG-MCA05S010, UT-NTNL0002]
- National Science Foundation [CHE-0822-935]
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [0822935] Funding Source: National Science Foundation
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Previous work by us showed that in replica exchange molecular dynamics, exchanges should be attempted extremely often, providing gains in efficiency and no undesired effects. Since that time some questions have been raised about the extendability of these claims to the general case. In this work, we answer this question in two ways. First, we perform a study measuring the effect of exchange attempt frequency in explicit solvent simulations including thousands of atoms. This shows, consistent with the previous assertion, that high exchange attempt frequency allows an optimal rate of exploration of configurational space. Second, we present an explanation of many theoretical and technical pitfalls when implementing replica exchange that cause improper exchanges resulting in erroneous data, exacerbated by high exchange attempt frequency.
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