Molecular dynamics simulations of biomolecules: Long-range electrostatic effects

被引:522
作者
Sagui, C [1 ]
Darden, TA [1 ]
机构
[1] Natl Inst Environm Hlth Sci, Res Triangle Pk, NC 27709 USA
来源
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE | 1999年 / 28卷
关键词
free energies; particle mesh Ewald; fast multipole; periodic boundary conditions; Ewald summation;
D O I
10.1146/annurev.biophys.28.1.155
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.
引用
收藏
页码:155 / 179
页数:25
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