MDScope — a visual computing environment for structural biology (original) (raw)

1995, Computer Physics Communications

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. ~ is expressly dedgned for distributed memory parallel architectures and uses a spatial decomposition parallelization ~ategy COUlfled with a multi-threaded, message-driven computation model which reduces inefficiencies due to communi¢~tlion latency. Through the MDCOMM software, vmd acts as a graphical interface and interactive control for namd, allowing a user running flamd 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. the study of biopolymer aggregates like membranes, and to protein structure prediction. Widely used MD applications include CHARMm [5], X,PLOR [8], GROMOS [29], AMBER [30], and CEDAR [10].