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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. [1]

22 relations: AMBER, CHARMM, Cygwin, Empirical valence bond, Force field implementation, Fortran, Free energy perturbation, GROMACS, GROMOS, Linux, List of software for molecular mechanics modeling, Microsoft Windows, Molecular design software, Molecular dynamics, Molecular modeling on GPUs, NAMD, OPLS, OS X, Sweden, Unix, Uppsala University, YASARA.

AMBER

AMBER (an acronym for Assisted Model Building with Energy Refinement) 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.

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CHARMM

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them.

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Cygwin

Cygwin is a Unix-like environment and command-line interface for Microsoft Windows.

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Empirical valence bond

The Empirical Valence Bond (EVB) approach (Warshel and Weiss 1980, 1981) is an approximation developed by Arieh Warshel to determine reaction free energies of enzymatic reactions by making the assumption that Rudy Marcus precise electron transfer theory of metals can be applied to electron transfers responsible for chemical catalysis in solution via a calibrated Hamiltonian.

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Force field implementation

This is a table of computer programs implementing molecular mechanics '''force fields'''.

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Fortran

Fortran (previously FORTRAN, derived from Formula Translating System) is a general-purpose, imperative programming language that is especially suited to numeric computation and scientific computing.

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Free energy perturbation

Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations.

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GROMACS

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

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GROMOS

GROMOS is a force field for molecular dynamics simulation developed at the University of Groningen and at at the at the ETH Zurich.

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Linux

Linux (pronounced or, less frequently) is a Unix-like and mostly POSIX-compliant computer operating system (OS) assembled under the model of free and open-source software development and distribution.

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List of software for molecular mechanics modeling

This is a list of computer programs that are predominantly used for molecular mechanics calculations.

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Microsoft Windows

Microsoft Windows (or simply Windows) is a metafamily of graphical operating systems developed, marketed, and sold by Microsoft.

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Molecular design software

Molecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.

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Molecular dynamics

Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules in the context of N-body simulation.

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Molecular modeling on GPUs

Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.

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NAMD

NAMD (NAnoscale Molecular Dynamics program) is a freeware molecular dynamics simulation package written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems (millions of atoms).

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OPLS

The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof.

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OS X

OS X (pronounced; originally Mac OS X) is a series of Unix-based graphical interface operating systems (OS) developed and marketed by Apple Inc. It is designed to run on Macintosh computers, having been pre-installed on all Macs since 2002.

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Sweden

Sweden (Sverige), officially the Kingdom of Sweden (Swedish), is a Scandinavian country in Northern Europe.

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Unix

Unix (all-caps UNIX for the trademark) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, developed in the 1970s at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and others.

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Uppsala University

Uppsala University (Uppsala universitet) is a research university in Uppsala, Sweden, and is the oldest university in Sweden and all of the Nordic countries, founded in 1477.

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YASARA

YASARA (acronym of Yet Another Scientific Artificial Reality Application) is a molecular visualisation, modelling, and dynamics program that can be used for a series of scientific applications as is expressed by the large number of mentioning this software.

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References

[1] https://en.wikipedia.org/wiki/Q_(software)

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