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: Seeing Molecular Machines in Action (June 2008)

image size: 117.5KB
made with VMD

Living cells are brimming with activity, much of it due to their manifold molecular machines pulling cargo, importing and exporting molecules, digesting food molecules and transforming their energy, reading and copying genetic messages, or synthesizing proteins from these messages (the latter done by the ribosome). Static structures of the molecular machines have been resolved through crystallography: machines pressed into the confinement of crystals and frozen into inactivity reveal their atomic level geometry through this methodology. However, many machines, for example the ribosome, undergo large conformational transitions during their cyclic action, but active motions are hard to view in atomic detail. A way out is offered by electron microscopy which freeze-shocks machines into states characteristic for action cycle intermediates. Unfortunately, the method does not yield atomic resolution images, leaving the chemical detail needed for a comprehension of the mechanisms blurred. Computational methods can be used to bridge the resolution gap: atomic level structures of non-functional states of the machines captured in crystals are deformed to match electron microscopy images. Until recently, the method worked well only for very small machines. Now a team of electron microscopists and computational biologists using NAMD extended the method to common size machines and reported its successful application to the ribosome, providing astonishing detail about ribosome dynamics and function. For more details, see our MDFF website.

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Spotlight: Seeing Molecular Machines in Action (June 2008)

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