NAMD - Scalable Molecular Dynamics

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Parallel Programming Laboratory

Bionumerics Research Group

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.

NAMD reference paper: Scalable molecular dynamics with NAMD.

Other Spotlights

Spotlight: Learning by Doing (June 2003)

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Modeling the molecular processes of biological cells is a craft and an art. Techniques like theoretical and computational skills can be learnt by training, but meaningful applications are achieved only with experience and sensitivity. A summer school in Theoretical and Computational Biophysics attempted to teach both the craft and art of modeling through learning by doing: nearly hundred participants from all over the world came for two weeks to the Beckman Institute in Illinois to stretch proteins, pull water through molecular channels, mine genomic data, build their own computer cluster, and study their favorate biomolecules. After lectures and discussions in the morning, afternoon and evening were devoted to learning by doing, assisted through 300 pages of tutorials, in computer laboratories humming with computational biology software, e.g., VMD, NAMD, and GAMESS, and linked to NCSA's fast pentium machines. The school lasted two weeks, but will go on much longer: all school materials remain available on the web; participants will use BioCoRE to stay in touch and continue the scholarship and friendship experienced in Illinois.

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