Extended ensemble approach for deriving transferable coarse-grained potentials

被引:107
作者
Mullinax, J. W. [1 ]
Noid, W. G. [1 ]
机构
[1] Penn State Univ, Dept Chem, University Pk, PA 16802 USA
关键词
MOLECULAR-DYNAMICS SIMULATION; MONTE-CARLO-SIMULATION; FORCE-FIELD; ATOMISTIC SIMULATIONS; BIOMOLECULAR SYSTEMS; MESOSCOPIC MODELS; SPIN-GLASSES; SOFT MATTER; PARALLEL; DEPENDENCE;
D O I
10.1063/1.3220627
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Coarse-grained (CG) models provide a computationally efficient means for investigating biological and soft-matter processes that evolve on long time scales and large length scales. The present work introduces an extended ensemble framework for calculating transferable CG potentials that accurately reproduce the structure of atomistic models for multiple systems. This framework identifies a generalized potential of mean force (PMF) as the appropriate CG potential for reproducing the structural correlations of an atomistic extended ensemble. A variational approach is developed for calculating transferable potentials that provide an optimal approximation to this PMF. Calculations for binary mixtures of alkanes and alcohols demonstrate that the extended ensemble potentials provide improved transferability relative to potentials calculated for a single system. (C) 2009 American Institute of Physics. [doi:10.1063/1.3220627]
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页数:13
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共 87 条
  • [1] Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains
    Allen, Erik C.
    Rutledge, Gregory C.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (03)
  • [2] A novel algorithm for creating coarse-grained, density dependent implicit solvent models
    Allen, Erik C.
    Rutledge, Gregory C.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (15)
  • [3] Anderson E, 1999, LAPACK USERS GUIDE, DOI [10.1137/1.9780898719604, DOI 10.1137/1.9780898719604]
  • [4] [Anonymous], 1997, Applied Numerical Linear Algebra
  • [5] Multiscale modeling of biomolecular systems: in serial and in parallel
    Ayton, Gary S.
    Noid, Will G.
    Voth, Gregory A.
    [J]. CURRENT OPINION IN STRUCTURAL BIOLOGY, 2007, 17 (02) : 192 - 198
  • [6] MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS
    BERG, BA
    NEUHAUS, T
    [J]. PHYSICAL REVIEW LETTERS, 1992, 68 (01) : 9 - 12
  • [7] Implicit solvent simulation models for biomembranes
    Brannigan, G
    Lin, LCL
    Brown, FLH
    [J]. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2006, 35 (02): : 104 - 124
  • [8] Transferability of coarse-grained force fields:: The polymer case
    Carbone, Paola
    Varzaneh, Hossein Ali Karimi
    Chen, Xiaoyu
    Mueller-Plathe, Florian
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (06)
  • [9] THE INVERSE PROBLEM IN CLASSICAL STATISTICAL-MECHANICS
    CHAYES, JT
    CHAYES, L
    LIEB, EH
    [J]. COMMUNICATIONS IN MATHEMATICAL PHYSICS, 1984, 93 (01) : 57 - 121
  • [10] ON THE VALIDITY OF THE INVERSE CONJECTURE IN CLASSICAL DENSITY FUNCTIONAL THEORY
    CHAYES, JT
    CHAYES, L
    [J]. JOURNAL OF STATISTICAL PHYSICS, 1984, 36 (3-4) : 471 - 488