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.

References

External links

* , at TCB website
NAMD page at the PPL website

Molecular dynamics software Science software {{science-software-stub

See also

References

External links