NAMD SCALABLE MOLECULAR DYNAMICS SOFTWARE

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. 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XT3 and IBM Blue Gene/L (neither platform supports dynamic linking and experience shows that binaries would be quickly out of date, so only source code is released).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.