Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality

Sanghyun Park; Fatemeh Khalili-Araghi; Emad Tajkhorshid; Klaus Schulten

doi:10.1063/1.1590311

Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality

Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, Klaus Schulten

Research output: Contribution to journal › Article › peer-review

Abstract

A method of free energy calculation based on Jarzynski's equality and the stiff-spring approximation is presented. Thus, this is applied to an steered molecular dynamics (SMD) simulation of the helix-coil transition of deca-alanine in vacuum. It is found that when only a limited number of trajectories of irreversible processes are available, the second order cumulant expansion yields the most accurate estimate, which can be further improved by using the unbiased estimate.

Original language	English (US)
Pages (from-to)	3559-3566
Number of pages	8
Journal	Journal of Chemical Physics
Volume	119
Issue number	6
DOIs	https://doi.org/10.1063/1.1590311
State	Published - Aug 8 2003

ASJC Scopus subject areas

Physics and Astronomy(all)
Physical and Theoretical Chemistry

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abstract = "A method of free energy calculation based on Jarzynski's equality and the stiff-spring approximation is presented. Thus, this is applied to an steered molecular dynamics (SMD) simulation of the helix-coil transition of deca-alanine in vacuum. It is found that when only a limited number of trajectories of irreversible processes are available, the second order cumulant expansion yields the most accurate estimate, which can be further improved by using the unbiased estimate.",

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