NAMD: A parallel, object oriented molecular dynamics program

被引：426

作者：

Nelson, MT ^{[1
]}

Humphrey, W ^{[1
]}

Gursoy, A ^{[1
]}

Dalke, A ^{[1
]}

Kale, LV ^{[1
]}

Skeel, RD ^{[1
]}

Schulten, K ^{[1
]}

机构：

[1] UNIV ILLINOIS, THEORET BIOPHYS GRP, BECKMAN INST 3111, URBANA, IL 61801 USA

来源：

INTERNATIONAL JOURNAL OF SUPERCOMPUTER APPLICATIONS AND HIGH PERFORMANCE COMPUTING | 1996年 / 10卷 / 04期

关键词：

D O I：

10.1177/109434209601000401

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed parallel multipole tree algorithm for full electrostatic force evaluation in O(N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illustrates the performance of NAMD.

引用

页码：251 / 268

页数：18

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