PORTING AND TESTING THE DESMOND MOLECULAR DYNAMICS CODE

这个子项目是许多研究子项目中的一个 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， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 启动分配要求移植和测试新开发的德斯蒙德分子动力学代码的克雷XT 3（Bigben）和Altix 4700（Pople）在匹兹堡超级计算中心。利用这一分配，PSC的科学家将与D。E. Shaw Research将该软件包免费提供给PSC系统的用户，用于非商业研究活动。Desmond使用新颖的并行算法和数值技术来实现生物分子系统的快速，可扩展的模拟，并使研究人员能够获得理解许多重要生物现象所需的更长时间尺度。在Cray XT 3上，有机会在低级门户网络接口上创建非常有效的Desmond实现。由于Desmond的新颖设计，预计将需要大量的努力来移植代码，以便在这些系统上有效地运行;然而，该项目的成功完成将为分子动力学研究界提供一个强大的工具，用于生物分子系统的长时间模拟。

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. A Startup allocation is requested for porting and testing the newly-developed Desmond molecular dynamics code to the Cray XT3 (Bigben) and Altix 4700 (Pople) at the Pittsburgh Supercomputing Center. Using this allocation, scientists at the PSC will work together with Desmond developers at D. E. Shaw Research to make the package freely available to users of PSC systems for non-commercial research activities. Desmond uses novel parallel algorithms and numerical techniques to enable the fast, scalable simulation of biomolecular systems and has enabled researchers to access the much longer timescales required to understand many important biological phenomena. On the Cray XT3 there is an opportunity to create a very efficient implementation of Desmond on the low-level Portals network interface. Due to the novel design of Desmond, it is anticipated that substantial effort will be required to port the code to run efficiently on these systems; however, successful completion of this project will provide the molecular dynamics research community with a powerful tool for the long time scale simulations of biomolecular systems.