Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer
software
Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications.
The history of software is closely tied to the development of digital comput ...
for
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...
simulation, written using the
Charm++ parallel programming model (not to be confused with
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CH ...
). It is noted for its parallel efficiency and is often used to simulate large systems (millions of
atom
Atoms are the basic particles of the chemical elements. An atom consists of a atomic nucleus, nucleus of protons and generally neutrons, surrounded by an electromagnetically bound swarm of electrons. The chemical elements are distinguished fr ...
s). It has been developed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the
University of Illinois Urbana–Champaign
The University of Illinois Urbana-Champaign (UIUC, U of I, Illinois, or University of Illinois) is a public land-grant research university in the Champaign–Urbana metropolitan area, Illinois, United States. Established in 1867, it is the fo ...
.
It was introduced in 1995 by Nelson ''et al.'' as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores.
NAMD has an interface to
quantum chemistry
Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions ...
packages
ORCA
The orca (''Orcinus orca''), or killer whale, is a toothed whale and the largest member of the oceanic dolphin family. The only extant species in the genus '' Orcinus'', it is recognizable by its black-and-white-patterned body. A cosmopol ...
and
MOPAC
MOPAC is a computational chemistry software package that implements a variety of semi-empirical quantum chemistry methods based on the neglect of diatomic differential overlap (NDDO) approximation and fit primarily for gas-phase thermochemistry ...
, as well as a scripted interface to many other quantum packages. Together with
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes ...
(VMD) and QwikMD, NAMD's interface provides access to hybrid
QM/MM
The hybrid QM/MM (quantum mechanics/molecular mechanics) approach is a molecular simulation method that combines the strengths of ''ab initio'' QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processe ...
simulations in an integrated, comprehensive, customizable, and easy-to-use suite.
NAMD is available as
freeware
Freeware is software, often proprietary, that is distributed at no monetary cost to the end user. There is no agreed-upon set of rights, license, or EULA that defines ''freeware'' unambiguously; every publisher defines its own rules for the free ...
for non-commercial use by individuals, academic institutions, and corporations for in-house business uses.
See also
*
Charm++
*
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
See also
*Car–Parrinello molecular dynamics
*Comparison of force-field implementations
*Comparison of nucleic acid simulation software
* ...
References
External links
* , at TCB website
NAMD page at the PPL website
Molecular dynamics software
Science software
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