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Calculating potentials of mean force from steered molecular dynamics simulations

J. Chem. Phys. 120, 5946 (2004); doi:10.1063/1.1651473

Issue Date: 1 April 2004

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Sanghyun Park and Klaus Schulten
Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
Steered molecular dynamics (SMD) permits efficient investigations of molecular processes by focusing on selected degrees of freedom. We explain how one can, in the framework of SMD, employ Jarzynski's equality (also known as the nonequilibrium work relation) to calculate potentials of mean force (PMF). We outline the theory that serves this purpose and connects nonequilibrium processes (such as SMD simulations) with equilibrium properties (such as the PMF). We review the derivation of Jarzynski's equality, generalize it to isobaric–isothermal processes, and discuss its implications in relation to the second law of thermodynamics and computer simulations. In the relevant regime of steering by means of stiff springs, we demonstrate that the work on the system is Gaussian-distributed regardless of the speed of the process simulated. In this case, the cumulant expansion of Jarzynski's equality can be safely terminated at second order. We illustrate the PMF calculation method for an exemplary simulation and demonstrate the Gaussian nature of the resulting work distribution. ©2004 American Institute of Physics.
History: Received 3 December 2003; accepted 7 January 2004
Permalink: http://link.aip.org/link/?JCPSA6/120/5946/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.He
    Biomolecular dynamics and conformational changes
  • 87.15.Aa
    Theory and modeling in molecular biophysics; computer simulation
  • 05.70.Ln
    Nonequilibrium and irreversible thermodynamics
  • 02.50.Ng
    Distribution theory and Monte Carlo studies
  • 31.15.Qg
    Molecular dynamics and other numerical methods (atoms and molecules)
  • YEAR: 2004

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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