MDScope - a visual computing environment for structural biology

Mark Nelson, William Humphrey, Richard Kufrin, Attila Gursoy, Andrew Dalke, Laxmikant V Kale, Robert Skeel, Klaus J Schulten

Research output: Contribution to journalArticle

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 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.

Original languageEnglish (US)
Pages (from-to)111-133
Number of pages23
JournalComputer Physics Communications
Volume91
Issue number1-3
DOIs
StatePublished - Sep 2 1995

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Keywords

  • Atomic and molecular dynamics

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Hardware and Architecture
  • Computer Science Applications

Cite this

Nelson, M., Humphrey, W., Kufrin, R., Gursoy, A., Dalke, A., Kale, L. V., Skeel, R., & Schulten, K. J. (1995). MDScope - a visual computing environment for structural biology. Computer Physics Communications, 91(1-3), 111-133. https://doi.org/10.1016/0010-4655(95)00045-H