TCB Publications - Abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope - A visual computing environment for structural biology. Computational Physics Communications, 91:111-134, 1995.

NELS95A MDScope is an integrated set of computational tools which function as an interactive visual computing environment for the simulation and study of biopolymers. 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. namd is expressly designed for distributed memory parallel architectures and uses a spatial decomposition parallelization strategy coupled with a multi-threaded, message-driven computation model which reduces inefficiencies due to communication latency. Through the MDCOMM software, vmd acts as a graphical interface and interactive control for namd, allowing a user running namd to utilize a parallel platform for computational power while visualizing the trajectory as it is computed. 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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