For more information on VMD and MDScope

 MDScope (a Molecular Dynamics computational environment) is a complete software environment for interactive simulation and display of biopolymers. It consists of three components:

• VMD
    A general molecular visualization program capable of interactive display and concurrent control of a molecular dynamics simulation running on a remote computer. VMD uses an object-oriented design, and is written in C++. This document describes the VMD component of MDScope.
• NAMD
    A molecular dynamics program designed specifically to run in parallel on a number of parallel computing platforms. NAMD employs the CHARMm energy function and accepts molecular structure and parameter files compatible with the program X-PLOR. NAMD fully supports connection to VMD, as well as a variety of molecular dynamics simulation options such as, and inclusion of complete long-range electrostatic forces through the use of the Fast Multipole Algorithm.
• MDComm
    A set of tools which allows fast, reliable communication and control between a molecular visualization program (such as VMD) and a molecular dynamics simulation program (such as NAMD). MDComm defines a protocol for transfer of static and dynamic molecular data between applications, provides a library for use by applications to send and receive this data, and includes daemons which coordinate and buffer the communication. Both VMD and NAMD use the MDComm software, which links these two applications into a single environment for interactive simulation of biomolecular assemblies.

For more information on MDScope, or on any of the individual components VMD, NAMD, or MDComm, see the Theoretical Biophysics Group WWW home page. Full source code and documentation for all components of MDScope may be obtained from the Theoretical Biophysics Group anonymous FTP server, in the directory pub/mdscope.