COMPUTATIONAL FACILITY

MDScope 建模环境 NAMD 的仿真组件 [19]，在功能和速度方面持续改进*。 最新版本，NAMD2（完全重写了 NAMD 的大部分内容） 代码），即将公开发布。 NAMD2 比任何其他产品都走得更远 先前版本在实现可修改性的 NAMD 设计目标方面， 速度和并行性能。 NAMD2 比 NAMD2 更具可修改性 原始版本，如上一版本中添加的功能所示 年。 该程序现在支持周期性边界条件，使用 截止静电或全埃瓦尔德静电。 它允许 使用三倍时间步进方案进行更大的模拟步骤，可以 允许某些模拟以原始速度的两倍运行 方法。 NAMD2 有一个基于 TCL 的脚本接口原型 允许用户更改模拟的某些部分，而无需 根本看一下程序代码。 现在还采用 DPME 全静电算法，由我们的合作者开发 杜克大学。 NAMD2支持大量并行机器， 包括工作站集群、SGI Origin 200 和 Origin 2000 年，IBM SP3、Convex Exemplar 和 Cray T3E。 新的 该程序的结构表现出改进的顺序速度，并且 在数十到数百台机器上更好的并行性能[22] 处理器。 改进的算法和并行效率，以及 大量处理器的可用性导致了订单 模拟速度大幅提高。

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.