TCB Publications - Abstract

Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. Journal of Chemical Physics, 119:3559-3566, 2003.

PARK2003A Jarzynski's equality is applied to free energy calculations from steered molecular dynamics simulations of biomolecules. The helix-coil transition of deca-alanine in vacuum is used as an example. With about ten trajectories sampled, the second order cumulant expansion, among the various averaging schemes examined, yields the most accurate estimates. We compare umbrella sampling and the present method, and find that their efficiencies are comparable.

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