Journal article
Multiscale implementation of infinite-swap replica exchange molecular dynamics
Proceedings of the National Academy of Sciences - PNAS, v 113(42), pp 11744-11749
18 Oct 2016
PMID: 27698148
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis-Hastings criterion. This guarantees that the joint distribution of the composite system of replicas is the normalized sum of the symmetrized product of the canonical distributions of these replicas at the different temperatures. Here we propose a different implementation of REMD in which (i) the swaps obey a continuous-time Markov jump process implemented via Gillespie's stochastic simulation algorithm (SSA), which also samples exactly the aforementioned joint distribution and has the advantage of being rejection free, and (ii) this REMD-SSA is combined with the heterogeneous multiscale method to accelerate the rate of the swaps and reach the so-called infinite-swap limit that is known to optimize sampling efficiency. The method is easy to implement and can be trivially parallelized. Here we illustrate its accuracy and efficiency on the examples of alanine dipeptide in vacuum and C-terminal β-hairpin of protein G in explicit solvent. In this latter example, our results indicate that the landscape of the protein is a triple funnel with two folded structures and one misfolded structure that are stabilized by H-bonds.
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Details
- Title
- Multiscale implementation of infinite-swap replica exchange molecular dynamics
- Creators
- Tang-Qing Yu - Courant Institute of Mathematical Sciences, New York University, New York, NY 10012Jianfeng Lu - Department of Mathematics, Duke University, Durham, NC 27708; Department of Physics, Duke University, Durham, NC 27708; Department of Chemistry, Duke University, Durham, NC 27708Cameron F Abrams - Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104Eric Vanden-Eijnden - Courant Institute of Mathematical Sciences, New York University, New York, NY 10012; eve2@cims.nyu.edu
- Publication Details
- Proceedings of the National Academy of Sciences - PNAS, v 113(42), pp 11744-11749
- Publisher
- PNAS; United States
- Grant note
- R01 GM100472 / NIGMS NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000385610400050
- Scopus ID
- 2-s2.0-84991687503
- Other Identifier
- 991014877955204721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Chemistry, Physical