PORTING AND BENCHMARKING OF THE AMBER MOLECULAR DYNAMICS SOFTWARE ON TERAGRID R

这个子项目是众多研究子项目之一

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. I am requesting a DAC award as teragrid roaming (30,000 SUs) in order to assist me in the further development of the AMBER molecular dyanmics software on various NSF resources. This includes testing and validation of AMBER 10 (due for release Mar 2008) on all NSF resources including Ranger. I plan to continue development of both parallel classical molecular dynamics but also to extend the performance and scalability of the QM/MM implementation in AMBER 10. The testing on as many platforms as possible is essential to ensuring a smooth release of the software. The benchmarks will be made available to the community via the AMBER website. In addition any performance improvements through porting will be incorporated in the release code for the entire AMBER community to benefit from. In addition to the above the purpose of this DAC request is also to do initial testing and benchmarking of the AMBER 10 code on various machines in order to support a large LRAC request that will be submitted in January for the March 08 LRAC.