Exactly Time-Reversible Molecular Dynamics Algorithm for Rigid-Body Systems

被引:1
|
作者
Kajima, Yasuhiro [1 ]
Hiyama, Miyabi [2 ]
Ogata, Shuji [1 ]
Tamura, Tomoyuki [1 ]
机构
[1] Nagoya Inst Technol, Grad Sch Engn, Nagoya, Aichi 4668555, Japan
[2] Nagoya Univ, Grad Sch Informat Sci, Nagoya, Aichi 4648601, Japan
基金
日本学术振兴会;
关键词
molecular dynamics; time reversibility; rigid body; rigid molecule; quaternion;
D O I
10.1143/JPSJ.80.114002
中图分类号
O4 [物理学];
学科分类号
0702 ;
摘要
A simple, time-reversible simulation algorithm for rigid molecules is proposed. No time-reversible simulation algorithm for rigid molecules as simple as the velocity-Verlet algorithm for point atoms has been devised owing to the complex mutual dependence of the angular position and the angular velocity. In the present algorithm, the time reversibility of the rotational motion of a rigid molecule is enforced at every time step by determining numerically the angular velocity required to satisfy its non linear equation. The numerical complexity and the stability of the present algorithm are compared with those of the former algorithms, including the symplectic one, through demonstrative simulation of a nanometer-sized water droplet. Despite the simplicity of the present algorithm, the total energy in the present algorithm is conserved well, as in the symplectic algorithm. The principal idea behind the present algorithm, to enforce the time reversibility numerically, is generally applicable to the numerical simulation of various time-evolution equations.
引用
收藏
页数:7
相关论文
共 50 条
  • [1] Fast time-reversible algorithms for molecular dynamics of rigid-body systems
    Kajima, Yasuhiro
    Hiyama, Miyabi
    Ogata, Shuji
    Kobayashi, Ryo
    Tamura, Tomoyuki
    JOURNAL OF CHEMICAL PHYSICS, 2012, 136 (23):
  • [2] Algorithm for rigid-body Brownian dynamics
    Gordon, Dan
    Hoyles, Matthew
    Chung, Shin-Ho
    PHYSICAL REVIEW E, 2009, 80 (06)
  • [3] Dynamics of Holonomic Rigid-Body Systems
    Yu. M. Andreev
    O. K. Morachkovskii
    International Applied Mechanics, 2005, 41 : 817 - 824
  • [4] Time-reversible ab initio molecular dynamics
    Niklasson, Anders M. N.
    Tymczak, C. J.
    Challacombe, Matt
    JOURNAL OF CHEMICAL PHYSICS, 2007, 126 (14):
  • [5] Dynamics of holonomic rigid-body systems
    Andreev, YM
    Morachkovskii, OK
    INTERNATIONAL APPLIED MECHANICS, 2005, 41 (07) : 817 - 824
  • [6] Time-reversible Born-Oppenheimer molecular dynamics
    Niklasson, Anders M. N.
    Tymczak, C. J.
    Challacombe, Matt
    PHYSICAL REVIEW LETTERS, 2006, 97 (12)
  • [7] Numerical irreversibility in time-reversible molecular dynamics simulation
    Komatsu, N
    Abe, T
    PHYSICA D-NONLINEAR PHENOMENA, 2004, 195 (3-4) : 391 - 397
  • [8] Time-reversible molecular dynamics algorithms with bond constraints
    Toxvaerd, Soren
    Heilmann, Ole J.
    Ingebrigtsen, Trond
    Schroder, Thomas B.
    Dyre, Jeppe C.
    JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (06):
  • [9] Rigid-body molecular dynamics of DNA inside a nucleosome
    Fathizadeh, Arman
    Besya, Azim Berdy
    Ejtehadi, Mohammad Reza
    Schiessel, Helmut
    EUROPEAN PHYSICAL JOURNAL E, 2013, 36 (03):
  • [10] Advanced gradientlike methods for rigid-body molecular dynamics
    Omelyan, Igor P.
    JOURNAL OF CHEMICAL PHYSICS, 2007, 127 (04):