MDSCOPE - A VISUAL COMPUTING ENVIRONMENT FOR STRUCTURAL BIOLOGY

MDScope is an integrated set of computational tools which function as an interactive visual computing environment for the simulation and stu dy 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 performa nce, 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 visua lization and simulation components of MDScope. namd is expressly desig ned for distributed memory parallel architectures and uses a spatial d ecomposition parallelization strategy coupled with a multi-threaded, m essage-driven computation model which reduces inefficiencies due to co mmunication latency. Through the MDCOMM software, vmd acts as a graphi cal interface and interactive control for namd, allowing a user runnin g namd to utilize a parallel platform for computational power while vi sualizing the trajectory as it is computed. Modularity in both vmd and namd is accomplished through an object-oriented design, which facilit ates the addition of features and new algorithms.