NAMD SCALABLE MOLECULAR DYNAMICS SOFTWARE

这个子项目是许多利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 NAMD（Nanoscale Molecular Dynamics，http：//www.ks.uiuc.edu/Research/namd/）是一种并行分子动力学代码，设计用于大型生物分子系统的高性能模拟[1，2]。 NAMD采用Charm++/匡威并行运行时系统（http：//charm.cs.uiuc.edu/）的优先级消息驱动执行功能，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以源代码和方便的预编译二进制文件的形式免费分发给20，000多名注册用户。 NAMD 2.6于2006年8月发布，已被超过4400名用户下载，其中800人是NIH资助的。此版本添加了用于Intel处理器上的Mac OS X的二进制文件和基于Cray XT 3和IBM Blue Gene/L的源代码（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，因此只发布源代码）。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，根据能量交换温度（或任何其他可脚本化的参数）。NAMD和psfgen结构构建工具都读取并解释了新的CHARMM 31流文件（结合了拓扑和参数）和新的CMAP交叉项（二面角-二面角）势函数。 位于德克萨斯州高级计算中心（TACC）的全新5000核Dell Infiniband群集于2006年11月可用于NAMD移植。这是资源可用的第一个基于Infiniband的主要群集。NAMD被迅速移植到机器上，串行性能非常出色，但由于MPI库的问题，直到最近并行扩展性才很差NAMD现在在机器上运行良好。更积极的并行性能调优针对Cray XT 3和IBM Blue Gene/L平台，包括将通信有效映射到Blue Gene/L环形网络的优化。通过粒子网格Ewald方法的二维分解，较大模拟的性能得到了改善，并且压缩分子结构以减少内存使用，从而允许数百万个原子的模拟适合256个Blue Gene/L上每个内核的可用内存为512 MB。 参考书目： [1]L.卡莱河Skeel，M.班达尔卡尔河Brunner，A. Gursoy，N.菲利普斯，A. Shinozaki，K. Varadarajan和K.舒尔滕NAMD 2：并行分子动力学的更大可扩展性。J. Comp. Phys.，151：283312，1999年。 [2]J. C.菲利普斯河Braun，W. Wang，J. Gumbart，E. Tajkhorshid，E.维拉角奇波特河D.斯基尔湖Kale和K.舒尔滕可缩放的分子动力学与NAMD。J. Comp. Chem.，二十六：一七八一1802年2005年。

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.