NAMD SCALABLE MOLECULAR DYNAMICS SOFTWARE

该子项目是利用NIH/NCRR资助的中心赠款提供的资源的许多研究子项目之一。子项目和研究者（PI）可能从另一个NIH来源获得主要资金，因此可以在其他CRISP条目中表示。所列机构为中心机构，不一定为研究者机构。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[44，113]。NAMD采用Charm++/匡威并行运行时系统（http：//charm.cs.uiuc.edu/）的优先消息驱动执行功能，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15，000多名注册用户。一份新的出版物[44]记录了NAMD的当前功能、算法和设计，并提供了从教程练习到[37]的大型多尺度模拟的应用示例。 NAMD 2.6b1于2005年7月发布，已被3600多名用户下载，其中650人是NIH资助的。此版本为Linux在Itanium、Altix和Opteron/Athlon 64/EMT 64上添加了二进制文件，并将IBM AIX上的串行性能提高了30%，Mac OS X上提高了70%。大，高度结合的结构，如共价晶体和稀疏的模拟，如粗粒度模型的模拟的内存使用量已大大减少，而不影响典型的生物聚合物模拟的性能。在Tcl中实现的新的自适应偏置力方法[115]通过应用自适应偏置力来提供均匀采样，有效地计算沿反应坐标沿着的平均力的潜力。随着新的基于Tcl的边界势，脚本力可以有效地单独施加到大量的原子。最后，OPLS力场现在得到支持。 匹兹堡超级计算中心（PSC）的新2000处理器Cray XT 3于2005年8月开始提供NAMD移植。由于XT 3采用了全新的互连和全新的操作系统，我们预计（并遇到）困难，但在Cray和PSC工作人员的帮助下，NAMD现在运行大多数功能（XT 3缺乏，例如，交互式模拟所需的套接字），并具有良好的性能和可伸缩性（调优将继续）。同样，圣地亚哥超级计算机中心（SDSC）的单机架BlueGene/L系统也可用，允许资源人员完成NAMD端口（以前仅用于性能调整）。这将是不可能分发NAMD二进制为克雷XT 3或BlueGene/L，因为由于缺乏动态链接在这个平台上的任何系统升级将需要重新编译。最后，NAMD已经被移植到新的Mac OS for Intel处理器和x86-64版本的Windows，两者都是原生的。

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 [44, 113]. NAMD employs the prioritized messagedriven 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 15,000 registered users as both source code and convenient precompiled binaries. A new publication [44] documents the current capabilities, algorithms, and design of NAMD and provides examples of applications ranging from a tutorial exercise to the large multiscale simulation of [37]. NAMD 2.6b1 was released in July 2005 and has been downloaded by over 3600 users, 650 of whom are NIH-funded. This release added binaries for Linux on Itanium, Altix, and Opteron/Athlon 64/EMT64 and improved serial performance by 30% on IBM AIX and 70% on Mac OS X. Memory usage for simulations of large, highly bonded structures such as covalent crystals and for sparse simulations such as coarse-grained models has been greatly reduced without affecting the performance of typical biopolymer simulations. The new Adaptive Biasing Force method [115], implemented in Tcl, efficiently calculates the potential of mean force along a reaction coordinate by applying adaptive biasing forces to provide uniform sampling. With new Tcl-based boundary potentials, scripted forces may be efficiently applied individually to large numbers of atoms. Finally, the OPLS force field is now supported. The new 2000-processor Cray XT3 at the Pittsburgh Supercomputing Center (PSC) became available for NAMD porting in August, 2005. As the XT3 employs both a completely new interconnect and a completely new operating system, we anticipated (and encountered) difficulties, but with assistance from Cray and PSC staff NAMD now runs with most features (the XT3 lacks, e.g., the sockets needed for interactive simulations) and with good performance and scalability (tuning continues). Similarly, the single-rack BlueGene/L system at the San Diego Supercomputer Center (SDSC) also became available, allowing the completion of the NAMD port (previously used only for performance tuning) by Resource personnel. It will be impossible to distribute NAMD binaries for the Cray XT3 or BlueGene/L since due to the lack of dynamic linking on this platforms any system upgrade would require recompilation. Finally, NAMD has been ported to the new Mac OS for Intel processors and to the x86-64 version of Windows, both natively for full performance.