NAMD SCALABLE MOLECULAR DYNAMICS SOFTWARE

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 NAMD(纳米级分子动力学，http://www.ks.uiuc.edu/Research/namd/))是为高性能模拟大型生物分子系统而设计的并行分子动力学程序[1，2]。NAMD采用Charge++/Converse并行运行时系统(http://charm.cs.uiuc.edu/)，)的优先消息驱动执行能力，允许在大规模并行超级计算机和商用工作站集群上进行出色的并行扩展。NAMD作为源代码和方便的预编译二进制文件免费分发给20,000多名注册用户。 NAMD 2.6于2006年8月发布，已有超过4400名用户下载，其中800名是由NIH资助的。此版本在英特尔处理器上为Mac OS X添加了二进制文件和源代码，以构建在Cray XT3和IBM Blue Gene/L之上(这两个平台都不支持动态链接，经验表明二进制文件很快就会过时，所以只发布源代码)。副本交换方法被实现为一组TCL脚本，这些脚本使用套接字连接来驱动一组NAMD作业，基于能量交换温度(或任何其他可编写脚本的参数)。NAMD和psfgen结构构建工具都读取和解释新的CHARMM 31流文件(结合了拓扑和参数)和新的CMAP交叉(二面体-二面体)势函数。 位于德克萨斯高级计算中心(TACC)的全新5000核Dell Infiniband群集于2006年11月可用于NAMD移植。这是该资源可用的第一个主要的基于Infiniband的群集。NAMD被迅速移植到机器上，并且串行性能很好，但是直到最近，由于MPI库的问题，并行可伸缩性很差NAMD现在机器上运行得很好。更积极的并行性能调优针对Cray XT3和IBM Blue gene/L平台，包括将通信高效地映射到Blue gene/L环形网络的优化。通过对粒子网格Ewald方法的二维分解，更大规模的模拟的性能得到了改善，通过压缩分子结构以减少内存使用量，可以在Blue gene/L上每个核心可用的256512MB内存中容纳数百万个原子的模拟。 参考书目： [1]L.Kale，R.Skeel，M.Bhandarkar，R.Brunner，A.Gursoy，N.Krawitz，J.Phillips，A.Shinozaki，K.Varadarajan和K.Schulten。NAMD2：并行分子动力学的更大可扩展性。J.Comp.物理，第151：283312,1999年。 [2]J.C.Phillips、R.Braun、W.Wang、J.Gumbart、E.Tajkhorshid、E.Villa、C.Chipot、R.D.Skeel、L.Kale和K.Schulten。使用NAMD的可扩展分子动力学。J.Comp.化学，2005年26：17811802。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. NAMD (Nanoscale Molecular Dynamics, http://www.ks.uiuc.edu/Research/namd/) is a parallel molecular dynamics code designed for high performance simulation of large biomolecular systems [1, 2]. NAMD employs the prioritized message-driven execution capabilities of the Charm++/Converse parallel runtime system (http://charm.cs.uiuc.edu/), allowing excellent parallel scaling on both massively parallel supercomputers and commodity workstation clusters. NAMD is distributed free of charge to over 20,000 registered users as both source code and convenient precompiled binaries. NAMD 2.6 was released in August 2006 and has been downloaded by over 4400 users, 800 of whom are NIH-funded. This release added binaries for Mac OS X on Intel processors and source code to build on the Cray XT3 and IBM Blue Gene/L (neither platform supports dynamic linking and experience shows that binaries would be quickly out of date, so only source code is released). The replica exchange method is implemented as a set of Tcl scripts that use socket connections to drive a set of NAMD jobs, exchanging temperatures (or any other scriptable parameter) based on energy. Both NAMD and the psfgen structure-building tool read and interpret the new CHARMM 31 stream files (combining topology and parameters) and the new CMAP crossterm (dihedral-dihedral) potential function. The new 5000-core Dell Infiniband cluster at the Texas Advanced Computing Center (TACC) became available for NAMD porting in November, 2006. This was the first major Infiniband-based cluster available to the Resource. NAMD was rapidly ported to the machine and serial performance was excellent, but parallel scaling was poor until recently due to issues with the MPI libraryNAMD now performs well on the machine. More aggressive parallel performance tuning has targeted the Cray XT3 and IBM Blue Gene/L platforms, including optimizations to map communication efficiently to the Blue Gene/L toroidal network. The performance of larger simulations has been improved by a two-dimensional decomposition of the particle-mesh Ewald method, and compression of the molecular structure to reduce memory usage allows multi-million-atom simultions to fit in the 256512MB of memory available per-core on the Blue Gene/L. Bibliography: [1] L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. NAMD2: Greater scalability for parallel molecular dynamics. J. Comp. Phys., 151:283312, 1999. [2] J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten. Scalable molecular dynamics with NAMD. J. Comp. Chem., 26:17811802, 2005.