2017-07-31T16:38:29+03:00[Europe/Moscow] en true GROMACS, [email protected], NAMD, Ascalaph Designer, LAMMPS, Q (software), CHARMM, AMBER, Amsterdam Density Functional, Avizo (software), YASARA, Tinker (software), GROMOS, SHARC molecular dynamics software, MacroModel, Molecular Modelling Toolkit, Tremolo-X, Abalone (molecular mechanics), Desmond (software) flashcards
Molecular dynamics software

Molecular dynamics software

  • GROMACS
    GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
  • [email protected] (FAH or [email protected]) is a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics.
  • NAMD
    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
    Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations.
  • LAMMPS
    Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories.
  • Q (software)
    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.
  • 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.
  • AMBER
    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
    Amsterdam Density Functional (ADF) is a program for first-principles electronic structure calculations that makes use of density functional theory (DFT).
  • Avizo (software)
    Avizo (pronounce: ‘a-VEE-zo’) is a general-purpose commercial software application for scientific and industrial data visualization and analysis.
  • YASARA
    Official website
  • Tinker (software)
    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
    GROMOS is the name of a force field for molecular dynamics simulation, and a related computer software package.
  • SHARC molecular dynamics software
    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
    MacroModel is a computer program for molecular modelling of organic compounds and biopolymers.
  • Molecular Modelling Toolkit
    The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.
  • Tremolo-X
    TREMOLO-X is a software package used for the numerical simulation of interactions between atoms and molecules, the molecular dynamics.
  • Abalone (molecular mechanics)
    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 (software)
    Desmond is a software package developed at D.