Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations

Journal of Computational Chemistry - Tập 30 Số 12 - Trang 1799-1815 - 2009
Séverine Queyroy1,2, Haruki Nakamura3, Ikuo Fukuda4,5
1Fujitsu Limited, 1-9-3 Nakase, Mihama-ku, Chiba 261-8588, Japan
2Laboratoire chimie Provence, chimie thorique, UMR 6264, Aix-Marseille Universités-CNRS Av. esc. Normandie-Niemen, Marseille 13397, France
3Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
4AIST, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan
5RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

Tóm tắt

AbstractThis article illustrates practical applications to molecular dynamics simulations of the recently developed numerical integrators [Phys Rev E 2006, 73, 026703] for ordinary differential equations. This method consists of extending any set of ordinary differential equations in order to define a time invariant function, and then use the techniques of divergence‐free solvable decomposition and symmetric composition to obtain volume‐preserving integrators in the extended phase space. Here, we have developed the technique by constructing multiple extended‐variable formalism in order to enhance the handling in actual simulation, and by constituting higher order integrators to obtain further accuracies. Using these integrators, we perform constant temperature molecular dynamics simulations of liquid water, liquid argon and peptide in liquid water droplet. The temperature control is obtained through an extended version of the Nosé‐Hoover equations. Analyzing the effects of the simulation conditions including time step length, initial values, boundary conditions, and equation parameters, we investigate local accuracy, global accuracy, computational cost, and sensitivity along with the sampling validity. According to the results of these simulations, we show that the volume‐preserving integrators developed by the current method are more effective than traditional integrators that lack the volume‐preserving property. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

Từ khóa


Tài liệu tham khảo

10.1103/PhysRevE.73.026703

10.1109/TNS.1983.4332919

10.1016/0375-9601(90)90092-3

10.1088/0951-7715/5/2/011

10.1006/jcph.1995.1172

10.1016/S0375-9601(98)00154-6

10.1103/RevModPhys.70.467

10.1080/00268978400101201

10.1103/PhysRevA.31.1695

10.1016/0375-9601(95)00973-6

10.1063/1.463940

10.1016/0003-4916(90)90124-7

10.1103/PhysRevA.34.2499

10.1002/jcc.20001

Gear C.W., 1971, Numerical Intitial Value Problems in Ordinary Differential Equations

10.1006/jcph.1998.6171

10.1063/1.448118

10.1103/PhysRevA.42.7467

10.1103/PhysRevE.64.056125

10.1209/epl/i2002-00196-9

Evans D. J., 1990, Statistical Mechanics of Non‐Equilibrium Liquids

Hoover W. G., 2001, Time Reversibility, Computer Simulation, and Chaos

10.1137/0916010

10.1007/978-3-662-05018-7

10.1016/S0377-0427(01)00492-7

10.1137/S0036142995281152

10.1063/1.445869

10.1002/jcc.540150109

10.1021/ja00124a002

10.1063/1.476919

10.1088/0305-4470/39/19/S01

10.1021/jp031086w

10.1006/jcph.1998.5879

10.1016/0009-2614(95)00316-V

10.1063/1.1389855

10.1137/S1064827596313851

Fukuda I.;Queyroy S.;Nakamura H.in preparation.

10.1016/S0375-9601(99)00899-3

10.1016/0021-9991(87)90148-3

Thông tin
Thông tin xuất bản

Journal of Computational Chemistry

Tập 30 Số 12

1799-1815

Thông tin tác giả