Multidimensional replica-exchange method for free-energy calculations

被引：702
|
作者：
Sugita, Y [1 ]
Kitao, A
Okamoto, Y
机构：
[1] Inst Mol Sci, Dept Theoret Studies, Aichi 4448585, Japan
[2] Kyoto Univ, Grad Sch Sci, Dept Chem, Kyoto 6068502, Japan
[3] Grad Univ Adv Studies, Dept Funct Mol Sci, Aichi 4448585, Japan
来源：
JOURNAL OF CHEMICAL PHYSICS | 2000年 / 113卷 / 15期
关键词：
D O I：
10.1063/1.1308516
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：
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method. (C) 2000 American Institute of Physics. [S0021- 9606(00)50739-9].
引用
收藏
页码：6042 / 6051
页数：10
相关论文
共 50 条
  • [11] Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules
    Oshima, Hiraku
    Re, Suyong
    Sugita, Yuji
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (10) : 5199 - 5208
  • [12] A convective replica-exchange method for sampling new energy basins
    Spill, Yannick G.
    Bouvier, Guillaume
    Nilges, Michael
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2013, 34 (02) : 132 - 140
  • [13] MULTIDIMENSIONAL FREE-ENERGY CALCULATIONS USING THE WEIGHTED HISTOGRAM ANALYSIS METHOD
    KUMAR, S
    ROSENBERG, JM
    BOUZIDA, D
    SWENDSEN, RH
    KOLLMAN, PA
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (11) : 1339 - 1350
  • [14] Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
    Jiang, Wei
    Roux, Benoit
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (09) : 2559 - 2565
  • [15] Replica-exchange-based free-energy methods.
    Essex, JW
    Woods, CJ
    Foucher, S
    King, MA
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2004, 227 : U1030 - U1030
  • [16] The development of replica-exchange-based free-energy methods
    Woods, CJ
    Essex, JW
    King, MA
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (49): : 13703 - 13710
  • [17] Replica-exchange extensions of simulated tempering method
    Mitsutake, A
    Okamoto, Y
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (06): : 2491 - 2504
  • [18] Replica-permutation method for biomolecules as a better alternative to replica-exchange method
    Itoh, S. G.
    Okumura, H.
    [J]. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2013, 42 : S91 - S91
  • [19] Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica-Exchange
    Wan, Shunzhou
    Tresadern, Gary
    Perez-Benito, Laura
    van Vlijmen, Herman
    Coveney, Peter, V
    [J]. ADVANCED THEORY AND SIMULATIONS, 2020, 3 (01)
  • [20] Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules
    Rieder, Salome R.
    Ries, Benjamin
    Schaller, Kay
    Champion, Candide
    Barros, Emilia P.
    Huenenberger, Philippe H.
    Riniker, Sereina
    [J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2022, 62 (12) : 3043 - 3056
12345