Gerhard Hummer 2005 New J. Phys. 7 34 doi:10.1088/1367-2630/7/1/034
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
Focus on Brownian Motion and Diffusion in the 21st CenturyGerhard Hummer
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Bayesian inference is used to obtain self-consistent estimates of free energies and position-dependent diffusion coefficients along complex reaction coordinates from molecular dynamics simulation trajectories. Effectively, exact solutions for the dynamics of a diffusive model are matched globally to the observed molecular dynamics data. The approach is first tested for a simple one-dimensional diffusion model, and then applied to the dihedral-angle dynamics of a peptide fragment dissolved in water. Both long equilibrium molecular dynamics simulations and short, appropriately initialized, replica simulations are used to sample the short-time dynamics of the peptide–water system. In both cases, accurate estimates of free energies and diffusion coefficients are obtained.
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Issue 1 (January 2005)
Received 28 September 2004
Published 31 January 2005
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Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
Gerhard Hummer 2005 New J. Phys. 7 34
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