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A skewed-momenta method to efficiently generate conformational-transition trajectories

By James MacFadyen and Ioan Andricioaei

Abstract

We present a novel computational method, the skewed-momenta method (Skew’M), which applies a bias to the Maxwell distribution of initial momenta used to generate ensembles of trajectories. As a result, conformational transitions are accentuated and kinetic properties are calculated more effectively. The connection to the related puddle jumping method is discussed. A reweighting scheme permits the exact calculation of kinetic properties. Applications are presented for the rapid calculation of rate constants for molecular isomerization, and for the efficient reconstruction of free-energy profiles using a straightforward modification of the Jarzynski identity

Publisher: The American Institute of Physics
Year: 2005
DOI identifier: 10.1063/1.2000242
OAI identifier: oai:deepblue.lib.umich.edu:2027.42/87860

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