STIFFNESS AND ENERGY-CONSERVATION IN MOLECULAR-DYNAMICS - AN IMPROVED INTEGRATOR

被引:87
作者
HARRISON, RW
机构
[1] Department of Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania
关键词
D O I
10.1002/jcc.540140912
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Molecular dynamics is the integration of a set of coupled differential equations describing the motion of atoms over time. These equations exhibit the unfortunate property of stiffness, that is, terms of the equations (the forces on the atoms) are defined on several scales-ranging from tens of kcal/mol/angstrom to thousands of kcal/mol/angstrom. Additional nonconservative and stiff effects occur when a distance cutoff is used for the electrostatics and nonbonded potentials. Because the first derivative at the cutoff is essentially infinite, small variations in positions will cause large variations in energy and violate conservation of energy. The effects are demonstrated in a small system of 125 isolated water molecules. It is possible to greatly reduce and nearly eliminate the stiff integration effects with an improved integrator. The nonconservative effects of the distance cutoff cannot be removed by changing the integrator. (C) 1993 by John Wiley & Sons, Inc.
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页码:1112 / 1122
页数:11
相关论文
共 16 条
[1]  
[Anonymous], 1987, DYNAMICS PROTEINS NU
[2]  
[Anonymous], 2012, PRACTICAL NUMERICAL
[3]  
Fletcher R., 1981, PRACTICAL METHODS OP
[4]  
Goldstein H., 1980, CLASSICAL MECH, V2nd ed
[5]   A CONSISTENT EMPIRICAL POTENTIAL FOR WATER-PROTEIN INTERACTIONS [J].
HERMANS, J ;
BERENDSEN, HJC ;
VANGUNSTEREN, WF ;
POSTMA, JPM .
BIOPOLYMERS, 1984, 23 (08) :1513-1518
[7]  
Knuth D.E., 1981, ART COMPUTER PROGRAM, V2
[8]  
Lanczos C., 1986, VARIATIONAL PRINCIPL
[9]   A UNIFIED FORMULATION OF THE CONSTANT TEMPERATURE MOLECULAR-DYNAMICS METHODS [J].
NOSE, S .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (01) :511-519
[10]   A POWERFUL TRUNCATED NEWTON METHOD FOR POTENTIAL-ENERGY MINIMIZATION [J].
SCHLICK, T ;
OVERTON, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1987, 8 (07) :1025-1039