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This seminar will present detailed information related to molecular mechanical methods of studying macromolecular motion. Areas of focus will include types of forcefields, topology and parameter files, electrostatics including the particle-mesh Ewald (PME) method, solvation models, coarse-grained methods, and techniques for analyzing results. The VMD and NAMD programs will be used throughout the seminar, both freely available, as well as the Biowulf Linux cluster here at NIH. The goal of the seminar is for a user to become versed to the point where a user can set up an MD simulation, run a simulation, and analyze results. A detailed hands-on exercise will be conducted.
This Molecular Dynamics Workshop is presented by the NIAID OCICB Bioinformatics and Computational Biosciences Branch (BCBB). For questions about the course or for collaboration on Molecular Dynamics problems, email BCBB at ScienceApps@niaid.nih.gov
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