AN EFFICIENT, BOX SHAPE INDEPENDENT NONBONDED FORCE AND VIRIAL ALGORITHM FOR MOLECULAR-DYNAMICS

被引：32

作者：

BEKKER, H ^{[1
]}

DIJKSTRA, EJ ^{[1
]}

RENARDUS, MKR ^{[1
]}

BERENDSEN, HJC ^{[1
]}

机构：

[1] UNIV GRONINGEN,BIOPHYS CHEM LAB,9747 AG GRONINGEN,NETHERLANDS

来源：

MOLECULAR SIMULATION | 1995年 / 14卷 / 03期

关键词：

MOLECULAR DYNAMICS SIMULATION; PERIODIC BOUNDARY CONDITIONS; NONBONDED FORCE; VIRIAL;

D O I：

10.1080/08927029508022012

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：

A notation is introduced and used to transform a conventional specification of the non-bonded force and virial algorithm in the case of periodic boundary conditions into an alternative specification. The implementation of the transformed specification is simpler and typically a factor of 1.5 faster than a conventional implementation. Moreover, it is generic with respect to the shape of the simulated system, i.e. the same routines can be used to handle triclinic boxes, truncated octahedron boxes etc. An implementation of this method is presented, and the speed achieved on various machines is given. Essence of the new method is that the number of calculations of image particle positions is strongly reduced during non-bonded force calculations.

引用

页码：137 / 151

页数：15