|
MDScope provides an interactive visual computing environment for the
simulation and study of biopolymers. The project implements standard
visualization and simulation methods and offers a foundation for testing
new algorithms and capabilities.
MDScope comprises two major software components:
- VMD - a visualization program for interactive display
and animation of molecules
- NAMD - a parallel, distributed-memory, molecular dynamics program
The programs can be used together or independently.
VMD and NAMD may be downloaded from their respective web pages,
are distributed free of charge, and include source code.
VMD
VMD is the molecular visualization component of MDScope. It provides
a wide variety of methods for rendering and coloring molecules and can
be used to animate and analyze the trajectory of a molecular dynamics
simulation. In addition, VMD can act as a graphical front end for an
external molecular dynamics program by displaying and animating a
molecule undergoing simulation on a remote computer.
For more information, see the VMD home page at
http://www.ks.uiuc.edu/Research/vmd/.
NAMD
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
For more information, see the NAMD home page at
http://www.ks.uiuc.edu/Research/namd/.
Publications
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope---A visual
computing environment for structural biology. In S.N. Atluri, G. Yagawa, and T.A.
Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995.
abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope---A visual
computing environment for structural biology. Computational Physics
Communications, 91:111-134, 1995.
abstract
William F. Humphrey, Andrew Dalke, and Klaus Schulten.
VMD - Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert D. Skeel, and Klaus Schulten. NAMD---A parallel, object-oriented
molecular dynamics program. International Journal of Supercomputer Applications
and High Performance Computing, 10:251-268, 1996.
abstract
L. V. Kalé, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki. NAMD: A Case Study in Multilingual Parallel Programming. In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag.
abstract,
postscript
James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. Avoiding algorithmic obfuscation in a message-driven parallel MD code. In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag.
abstract,
postscript
Robert Brunner, Laxmikant Kalé, and James Phillips. Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code. In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.
Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999.
abstract,
postscript
|
