NAMD

[[Category: Molecular Dynamics, Chemistry, Biology]

Description

NAMD website  

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.

Required Modules

Modules documentation

Parallel

• intel
• openmpi
• fftw
• namd

Parallel with CUDA Support

• intel
• openmpi
• fftw
• cuda
• namd

PBS Script Examples

See the NAMD_PBS page for NAMD PBS script example.

Citation

If you publish research that uses NAMD you may want to cite it as follows:

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal