MOLECULAR MODELING: PROGRAM NAMD

分子建模：NAMD 程序

• 批准号: 6295234
• 负责人: MILIND BHANDARKAR
• 金额: $ 23.13万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-02-01 至 1999-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6295234
• 关键词: bioengineering /biomedical engineering; biomedical resource; computers; statistics /biometry; structural biology; technology /technique

The simulation component of the MDScope modeling environment, NAMD [19], continues to undergo improvement in both features and speed*. The latest version, NAMD2 (a complete rewrite of much of the NAMD code), is nearing a public release. NAMD2 goes further than any previous release in achieving the NAMD design goals of modifiability, speed, and parallel performance. NAMD2 is more modifiable than the original version, as demonstrated by the features added in the last year. The program now supports periodic boundary conditions, using either cutoff electrostatics or full Ewald electrostatics. It allows larger simulation steps using a triple-time-stepping scheme, which can allow some simulations to run at double the speed of the original method. NAMD2 has a prototype TCL-based scripting interface that permits users to alter some parts of the simulation without having to look at the program code at all. It now also employs the DPME algorithm for full electrostatics, developed by our collaborators at Duke University. NAMD2 supports a large number of parallel machines, including clusters of workstations, the SGI Origin 200 and Origin 2000, the IBM SP3, the Convex Exemplar, and the Cray T3E. The new structure of the program exhibits improved sequential speed, and better parallel performance [22] on machines with dozens to hundreds of processors. Improved algorithms and parallel efficiency, and the availability of large numbers of processor have resulted in an order of magnitude increase in the speed of simulations.

MDScope建模环境NAMD的仿真组件 [19]，在功能和速度方面都在不断改进 *。 最新版本NAMD 2（完全重写了NAMD的大部分内容） 代码），即将公开发布。 NAMD2比任何 在实现NAMD可修改性设计目标方面， 速度和并行性能。 NAMD 2比 原始版本，如上一个版本中添加的功能所示 年 程序现在支持周期性边界条件，使用 无论是截止静电还是完全埃瓦尔德静电。 它允许 更大的模拟步骤，使用三重时间步进方案，可以 允许一些模拟以原来的两倍速度运行 法 NAMD2有一个基于TCL的原型脚本接口， 允许用户更改模拟的某些部分，而无需 看看程序代码。 它现在还雇用DPME 完全静电的算法，由我们的合作者在 杜克大学。 NAMD 2支持大量并行机， 包括工作站集群、SGI Origin 200和Origin 2000年，IBM SP3，凸范例，和克雷T3E。 新 程序的结构表现出改进的顺序速度，并且 更好的并行性能[22]在机器上有几十到几百个 的处理器。 改进的算法和并行效率， 大量处理器的可用性导致了订单 在模拟速度上的巨大提升。