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Simplifying molecular dynamics on the Biowulf Cluster using the NAMD server at NIH

Tuesday, October 25, 2011 — Poster Session II

Noon – 2:00 p.m.

Natcher Conference Center




  • S Orlow
  • S Chacko
  • M Dolan
  • D Hoover
  • D Hurt
  • V Gopalan


NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It can scale to hundreds of processors using fast interconnect networks such as Infiniband. While experienced users can create complex methods of refinement and modeling, it is a struggle for new or infrequent users to perform basic molecular dynamic methods. Moreover, because such methods can last for thousands to millions of CPU hours, making a mistake in the method is costly and an inefficient use of scarce computational resources. To address this problem, a Web-based interface to NAMD on the NIH Biowulf Cluster has been developed to facilitate basic molecular dynamics simulations. These include energy minimization, equilibration, and simulated annealing. The user need only upload a protein structure, choose a method, modify a few standard input parameters and submit the job. The job is queued, and an interface is available for following the progress and stopping the job if necessary. Final result files are compressed in a format suitable for download, and job data is retained for two months. The NAMD Server is a useful tool for assessing the validity of a modeled structure or preparing a protein model for downstream studies.

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