Perspective: Computer simulations of long time dynamics

被引:53
|
作者
Elber, Ron [1 ]
机构
[1] Univ Texas Austin, Inst Computat Engn & Sci, Dept Chem, Austin, TX 78712 USA
来源
JOURNAL OF CHEMICAL PHYSICS | 2016年 / 144卷 / 06期
关键词
ATOMICALLY DETAILED SIMULATIONS; MOLECULAR-DYNAMICS; FOLDING PATHWAYS; SPECIAL-PURPOSE; STRING METHOD; TRANSITION; TRAJECTORIES; KINETICS; COMPUTATION; ALGORITHMS;
D O I
10.1063/1.4940794
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
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. (C) 2016 AIP Publishing LLC.
引用
收藏
页数:12
相关论文
共 50 条
  • [21] Conformational Dynamics of Dopamine β-Hydroxylase by Computer Simulations
    Besch, Alida
    Cembran, Alessandro
    BIOPHYSICAL JOURNAL, 2018, 114 (03) : 49A - 49A
  • [23] COMPUTER-SIMULATIONS OF NUCLEAR-DYNAMICS
    BOAL, DH
    ANNUAL REVIEW OF NUCLEAR AND PARTICLE SCIENCE, 1987, 37 : 1 - 31
  • [24] Long range corrections for computer simulations of adsorption
    Siperstein, F
    Myers, AL
    Talu, O
    MOLECULAR PHYSICS, 2002, 100 (13) : 2025 - 2030
  • [25] Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning
    Narayan, Brajesh
    Yuan, Ye
    Fathizadeh, Arman
    Elber, Ron
    Buchete, Nicolae-Viorel
    COMPUTATIONAL APPROACHES FOR UNDERSTANDING DYNAMICAL SYSTEMS: PROTEIN FOLDING AND ASSEMBLY, 2020, 170 : 215 - 237
  • [26] Brownian dynamics in Fourier space: Membrane simulations over long length and time scales
    Lin, LCL
    Brown, FLH
    PHYSICAL REVIEW LETTERS, 2004, 93 (25)
  • [27] MBO(N)D: A multibody method for long-time molecular dynamics simulations
    Chun, HM
    Padilla, CE
    Chin, DN
    Watanabe, M
    Karlov, VI
    Alper, HE
    Soosaar, K
    Blair, KB
    Becker, OM
    Caves, LSD
    Nagle, R
    Haney, DN
    Farmer, BL
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2000, 21 (03) : 159 - 184
  • [28] Shadow Hamiltonian in classical NVE molecular dynamics simulations: A path to long time stability
    Hammonds, K. D.
    Heyes, D. M.
    JOURNAL OF CHEMICAL PHYSICS, 2020, 152 (02):
  • [29] Molecular dynamics computer simulations of solvation dynamics at liquid/liquid interfaces
    Michael, D
    Benjamin, I
    JOURNAL OF CHEMICAL PHYSICS, 2001, 114 (06): : 2817 - 2824