NAMD

/NAMD
NAMD2019-08-04T14:17:07+04:30

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, 24 years ago
  • 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. 

www.ks.uiuc.edu

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