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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.
Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999