MDScope - a visual computing environment for structural biology

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

Research output: Contribution to journalArticlepeer-review


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
Issue number1-3
StatePublished - Sep 2 1995


  • Atomic and molecular dynamics

ASJC Scopus subject areas

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


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