Implicit-solvent models have reduced the computational costs in conformational sampling but molecular dynamics simulations using such models do not carry the correct dynamical information.  Stochastic simulations provide one way to put back time information approximately.  We are particularly interested in using fast approximate methods to estimate time scale in applications that rough estimate of time scale is already useful.  These methods are based on Brownian dynamics and can be implemented in different ways such as using the Ermak-McCammon algorithm or the Feynman path integral formalism.  We shall illustrate the applications of these methods to studying ion dynamics surrounding biological molecules, peptide dynamics, and drug-binding kinetics.

Estimating time scale in implicit-solvent biomolecular simulations

248th National Meeting (2014)

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