NAnoscale Molecular Dynamics (NAMD)
NAMD is a computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems.
- Developer(s): University of Illinois at Urbana–Champaign, Theoretical and Computational Biophysics Group (TCB), Parallel Programming Laboratory (PPL).
- Initial release: 1995,
- Repository: charm
.cs .illinois .edu /gerrit /namd .git
- Written in: C++
- Operating system: Cross-platform; Windows, Linux, macOS, Unix
- Platform: x86, x86-64
- Available in: English
- License: Proprietary, freeware for noncommercial use
- Website: www
.ks .uiuc .edu /Research /namd
processes of Building NAMD input files and running the simulation
In order to run any MD simulation, NAMD requires at least four things:
- a Protein Data Bank (pdb) file which stores atomic coordinates and/or velocities for the system. Pdb files may be generated by hand, but they are also available via the Internet for many proteins at http://www.pdb.org.
- a Protein Structure File (psf) which stores structural information of the protein, such as various types of bonding interactions.
- a force field parameter file. A force field is a mathematical expression of the potential which atoms in the system experience. CHARMM, X-PLOR, AMBER, and GROMACS are four types of force fields, and NAMD is able to use all of them. The parameter file defines bond strengths, equilibrium lengths, etc.
- a configuration file, in which the user specifies all the options that NAMD should adopt in running a simulation. The configuration file tells NAMD how the simulation is to be run.