![]() ![]() These script-based facilities simplify the process of adding complex forces to systems and implementing boundary conditions. This tutorial is designed to guide users of VMD and NAMD in the use of the tclForces and tclBC scripts. User-Defined Forces in NAMD ( html) ( pdf, 4.3M ) ( required tutorial files, , individual files).Skeel, Laxmikant Kale, and Klaus Schulten. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. The physical concepts behind NAMD along with the programs design and algorithms are described in this publication that we recommend highly for study along with working through the above NAMD tutorial: Scalable molecular dynamics with NAMD. Tutorial versions available for Windows, or Mac and Unix/Linux platforms. Participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files, with an emphasis on such files for protein energy minimization and equilibration in water. ( required tutorial files (all platforms), , individual files (all platforms)) ( html for Windows) ( pdf for Windows, 6.8M) ( html for Unix/Mac) ( pdf for Unix/Mac, 8.3M) Be sure you have the latest version of NAMD. The tutorials below focus on NAMD-specific features, although many other tutorials utilize NAMD as well.
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