MDScope - a visual computing environment for structural biology

We describe the program MDScope, an integrated set of computational tools which function as an interactive visual computing environment for the simulation and study of biopoly-mers. This environment consists of three parts: (1) vmd, a molecular visualization program for interactive display of molecular systems; (2) namd, a molecular dynamics program designed for performance, scalability, modularity, and portability, which runs in parallel on a variety of computer platforms; (3) MDCOMM, a protocol and library which functions as the unifying communication agent between the visualization and simulation components of MDScope. Modularity in both vmd and namd is accomplished through an object-oriented design, which facilitates the addition of features and new algorithms.

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