期刊
JOURNAL OF CHEMICAL PHYSICS
卷 126, 期 14, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.2716389
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资金
- NCRR NIH HHS [RR020889] Funding Source: Medline
- NIGMS NIH HHS [GM59796] Funding Source: Medline
A recently introduced computational algorithm to extend time scales of atomically detailed simulations is illustrated. The algorithm, milestoning, is based on partitioning the dynamics to a sequence of trajectories between milestones and constructing a non-Markovian model for the motion along a reaction coordinate. The kinetics of a conformational transition in a blocked alanine is computed and shown to be accurate, more efficient than straightforward molecular dynamics by a factor of about 9, and nonexponential. A general scaling argument predicts a linear speedup with the number of milestones for diffusive processes and an exponential speedup for transitions over barriers. The algorithm is also trivial to parallelize. As a side result, milestoning also produces the free energy profile along the reaction coordinate and is able to describe nonequilibrium motions along one (or a few) degrees of freedom. (c) 2007 American Institute of Physics.
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