Journal
JOURNAL OF COMPUTATIONAL PHYSICS
Volume 231, Issue 6, Pages 2565-2580Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jcp.2011.12.007
Keywords
Molecular dynamics; Metropolis-Hastings; Verlet; RATTLE; RESPA
Funding
- NSF [DMS-0803095, DMS-0718172, DMS-0708140]
- ONR [N00014-04-1-6046]
- Division Of Mathematical Sciences
- Direct For Mathematical & Physical Scien [1114827] Funding Source: National Science Foundation
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This paper extends the results in [8] to stochastic differential equations (SDEs) arising in molecular dynamics. It implements a patch to explicit integrators that consists of a Metropolis-Hastings step. The 'patched integrator' preserves the SDE's equilibrium distribution and is accurate on finite time intervals. As a corollary this paper proves the integrator's accuracy in estimating finite-time dynamics along an infinitely long solution - a first in molecular dynamics. The paper also covers multiple time-steps, holonomic constraints and scalability. Finally, the paper provides numerical tests supporting the theory. (C) 2011 Elsevier Inc. All rights reserved.
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