MDScope - A visual Computing Environment for Structural Biology
| M. Nelson | Attila Gursoy | A. Dalke | Laxmikant Kale | Robert Skeel | Klaus Schulten | R. Kuffrin
Computer Physics Communications 1995
Publication Type: Paper
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Abstract
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 plat- forms; (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.
TextRef
M.Nelson and W. Humprey A. Gursoy and A. Dalke and L.V. Kale and R Skeel and K. Schulten and R. Kuffrin, "MDScope-A visual COmputing Environment for Structural Biology.", Computer Physics Communications, vol. 91, October 1995, pp. 111-134.
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