Non-iterative and exact method for constraining particles in a linear geometry

被引:7
作者
Tapia-McClung, H [1 ]
Gronbech-Jensen, N [1 ]
机构
[1] Univ Calif Davis, Dept Appl Sci, Davis, CA 95616 USA
关键词
molecular dynamics; molecular modeling; simulations; modeling;
D O I
10.1002/polb.20383
中图分类号
O63 [高分子化学(高聚物)];
学科分类号
070305 ; 080501 ; 081704 ;
摘要
We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations and is limited in accuracy only by the numerical methods for solving small systems of linear equations. As a result of the non-iterative and exact (within numerical accuracy) nature of the procedure, there is no drift in the constrained geometry, and the method is therefore readily applied to molecular dynamics simulations of, for example, rigid linear molecules or materials of non-spherical grains. We illustrate the approach through implementation in the commonly used second-order velocity-explicit Verlet method. (c) 2005 Wiley Periodicals, Inc.
引用
收藏
页码:911 / 916
页数:6
相关论文
共 14 条
[1]  
Allen M. P., 1990, COMPUTER SIMULATION
[3]   MOLECULAR-DYNAMICS OF RIGID SYSTEMS IN CARTESIAN COORDINATES A GENERAL FORMULATION [J].
CICCOTTI, G ;
FERRARIO, M ;
RYCKAERT, JP .
MOLECULAR PHYSICS, 1982, 47 (06) :1253-1264
[4]   CONSTRAINED MOLECULAR-DYNAMICS - SIMULATIONS OF LIQUID ALKANES WITH A NEW ALGORITHM [J].
EDBERG, R ;
EVANS, DJ ;
MORRISS, GP .
JOURNAL OF CHEMICAL PHYSICS, 1986, 84 (12) :6933-6939
[5]   Rigid molecular model for the assembly characteristics and optimal structure in molecular monolayers of alkanethiols on Au(111) [J].
Gronbech-Jensen, N ;
Parikh, AN ;
Beardmore, KM ;
Desai, RC .
LANGMUIR, 2003, 19 (05) :1474-1485
[6]  
Krautler V., 2001, Journal of Computational Chemistry, V22, P501, DOI 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO
[7]  
2-V
[8]  
LEACH AR, 2001, MOL MODELLING
[9]   SETTLE - AN ANALYTICAL VERSION OF THE SHAKE AND RATTLE ALGORITHM FOR RIGID WATER MODELS [J].
MIYAMOTO, S ;
KOLLMAN, PA .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1992, 13 (08) :952-962
[10]   NUMERICAL-INTEGRATION OF CARTESIAN EQUATIONS OF MOTION OF A SYSTEM WITH CONSTRAINTS - MOLECULAR-DYNAMICS OF N-ALKANES [J].
RYCKAERT, JP ;
CICCOTTI, G ;
BERENDSEN, HJC .
JOURNAL OF COMPUTATIONAL PHYSICS, 1977, 23 (03) :327-341