Flashcards: Molecular dynamics software

GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.

Folding@home (FAH or F@h) is a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics.

Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model.

Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations.

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories.

Q is a molecular dynamics (MD) simulation package which, unlike other MD codes, has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations.

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.

Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco.

Amsterdam Density Functional (ADF) is a program for first-principles electronic structure calculations that makes use of density functional theory (DFT).

Avizo (pronounce: ‘a-VEE-zo’) is a general-purpose commercial software application for scientific and industrial data visualization and analysis.

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Tinker, stylized as TINKER, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers.

GROMOS is the name of a force field for molecular dynamics simulation, and a related computer software package.

SHARC (Surface Hopping including ARbitrary Couplings) is an ab initio molecular dynamics program suite primarily dedicated to study the excited-state dynamics of molecules.

MacroModel is a computer program for molecular modelling of organic compounds and biopolymers.

The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.

TREMOLO-X is a software package used for the numerical simulation of interactions between atoms and molecules, the molecular dynamics.

Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models.

Desmond is a software package developed at D.