Optimizing replica exchange moves for molecular dynamics

被引：21
|
作者：
Nadler, Walter [1 ]
Hansmann, Ulrich H. E.
机构：
[1] Forschungszentrum Julich, John Von Neumann Inst Comp, D-52425 Julich, Germany
[2] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA
来源：
PHYSICAL REVIEW E | 2007年 / 76卷 / 05期
关键词：
D O I：
10.1103/PhysRevE.76.057102
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 sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.
引用
收藏
页数：4
相关论文
共 50 条
  • [1] Velocity scaling for optimizing replica exchange molecular dynamics
    Kouza, Maksim
    Hansmann, Ulrich H. E.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2011, 134 (04):
  • [2] Replica Exchange Molecular Dynamics
    Peng, Cheng
    Wu, Leyun
    Xu, Zhijian
    Zhu, Weiliang
    [J]. PROGRESS IN CHEMISTRY, 2022, 34 (02) : 384 - 396
  • [3] Exchange frequency in replica exchange molecular dynamics
    Sindhikara, Daniel
    Meng, Yilin
    Roitberg, Adrian E.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (02):
  • [4] Convergence of replica exchange molecular dynamics
    Zhang, W
    Wu, C
    Duan, Y
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2005, 123 (15):
  • [5] Exchange Often and Properly in Replica Exchange Molecular Dynamics
    Sindhikara, Daniel J.
    Emerson, Daniel J.
    Roitberg, Adrian E.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (09) : 2804 - 2808
  • [6] An optimized replica exchange molecular dynamics method
    Kamberaj, Hiqmet
    van der Vaart, Arjan
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (07):
  • [7] Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning
    Dashti, Danial Sabri
    Roitberg, Adrian E.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9 (11) : 4692 - 4699
  • [8] A canonical replica exchange molecular dynamics implementation with normal pressure in each replica
    Peter, Emanuel K.
    Pivkin, Igor V.
    Shea, Joan-Emma
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2016, 145 (04):
  • [9] Replica exchange molecular dynamics simulations of reversible folding
    Rao, F
    Caflisch, A
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2003, 119 (07): : 4035 - 4042
  • [10] Optimization and convergence metrics for replica exchange molecular dynamics
    Roitberg, Adrian E.
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2007, 234
12345