namd (Not just Another Molecular Dynamics program)
- author
- A. Dalke, A. Gursoy, W. Humphrey, L. Kale, M. Nelson
- abstract
-
The program namd is a prallel, object-oriented molecular dynamics program
designed for efficiency, protability, and modularity. A general structure
based on a small set of generic object for communication between processors,
calculation of atomic forces, and integration of the equations of motion
allows namd to adopt different algorithms for these aspects of the molecular
dynamics calculation.
The program uses a spatial decomposition to distribute atoms among processors.
The model is broken down into uniform cubes of space referred to as pathces.
A set of pathces are assigned to each processor. Pathces are dynamically
redistributed during the simulation to achieve better load-balancing.
The program is message driven, meaning that the order of computation
is determined by the arrival of messages indicating that the data
necessary for a given computation is available. This type of scheduling
of tasks allows for the greatest possible overlap of communication and
computation times. namd uses the same force field and input files as
the program X-PLOR. It will also produce binary DCD trajectory files and
will be able to interact with the graphical display program VMD.
- description
- http://www.ks.uiuc.edu:1250/Research/namd/namd.html
- reference
- http:/~nelson/prog_guide.ps
- contact
- nelson@ks.uiuc.edu, gursoy@ks.uiuc.edu
- keywords
- application program
- publication-date
- 09 February 1995
- application
- molecular dynamics, theoretical biophysics