Simultaneous computation of free energies and kinetics of rare events

被引:36
作者
Moroni, D
van Erp, TS
Bolhuis, PG
机构
[1] Univ Amsterdam, Hoff Inst Mol Sci, NL-1018 WV Amsterdam, Netherlands
[2] Ecole Normale Super Lyon, Phys Lab, Ctr Europeen Calcul Atom & Mol, F-69364 Lyon, France
来源
PHYSICAL REVIEW E | 2005年 / 71卷 / 05期
关键词
D O I
10.1103/PhysRevE.71.056709
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
We introduce a method to evaluate simultaneously the reaction rate constant and the free energy profile of a process in a complex environment. The method employs the partial path transition interface sampling technique we recently developed for the calculation of rate constants in diffusive systems. We illustrate the applicability of the technique by studying a simple dimer in a repulsive fluid, and show that the free energy can be obtained at no additional computational cost.
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页数:5
相关论文
共 11 条
  • [1] Bennett C. H., 1977, ACS S SERIES, V46
  • [2] Transition-path sampling of β-hairpin folding
    Bolhuis, PG
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (21) : 12129 - 12134
  • [3] STATISTICAL-MECHANICS OF ISOMERIZATION DYNAMICS IN LIQUIDS AND TRANSITION-STATE APPROXIMATION
    CHANDLER, D
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1978, 68 (06) : 2959 - 2970
  • [4] On the calculation of reaction rate constants in the transition path ensemble
    Dellago, C
    Bolhuis, PG
    Chandler, D
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (14) : 6617 - 6625
  • [5] Transition path sampling
    Dellago, C
    Bolhuis, PG
    Geissler, PL
    [J]. ADVANCES IN CHEMICAL PHYSICS, VOL 123, 2002, 123 : 1 - 78
  • [6] HYBRID MONTE-CARLO
    DUANE, S
    KENNEDY, AD
    PENDLETON, BJ
    ROWETH, D
    [J]. PHYSICS LETTERS B, 1987, 195 (02) : 216 - 222
  • [7] Computing time scales from reaction coordinates by milestoning
    Faradjian, AK
    Elber, R
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (23) : 10880 - 10889
  • [8] Frenkel D., 2000, Computational Science Series
  • [9] Rate constants for diffusive processes by partial path sampling
    Moroni, D
    Bolhuis, PG
    van Erp, TS
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (09) : 4055 - 4065
  • [10] MORONI D, 2005, THESIS U AMSTERDAM, P50601