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34 relations: AMBER, CHARMM, Comparison of force field implementations, Comparison of software for molecular mechanics modeling, Cygwin, Electrostatics, Empirical valence bond, Fortran, Free energy perturbation, GNU General Public License, GROMACS, GROMOS, Linux, MacOS, Microsoft Windows, Molecular design software, Molecular dynamics, Molecular modeling on GPUs, NAMD, Nucleic acid, Open-source model, OPLS, Path integral formulation, Protein, Software, Solution, Solvent, Sweden, Unix, Uppsala University, Van der Waals force, X86, X86-64, YASARA.
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.
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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.
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Comparison of force field implementations
This is a table of computer programs implementing molecular mechanics force fields.
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Comparison 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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Cygwin
Cygwin is a Unix-like environment and command-line interface for Microsoft Windows.
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Electrostatics
Electrostatics is a branch of physics that studies electric charges at rest.
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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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Fortran
Fortran (formerly FORTRAN, derived from Formula Translation) is a general-purpose, compiled 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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GNU General Public License
The GNU General Public License (GNU GPL or GPL) is a widely used free software license, which guarantees end users the freedom to run, study, share and modify the software.
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GROMACS
GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
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GROMOS
GROMOS is the name of a force field for molecular dynamics simulation, and a related computer software package.
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Linux
Linux is a family of free and open-source software operating systems built around the Linux kernel.
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MacOS
macOS (previously and later) is a series of graphical operating systems developed and marketed by Apple Inc. since 2001.
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Microsoft Windows
Microsoft Windows is a group of several graphical operating system families, all of which are 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 method for studying the physical movements of atoms and molecules.
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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
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model.
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Nucleic acid
Nucleic acids are biopolymers, or small biomolecules, essential to all known forms of life.
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Open-source model
The open-source model is a decentralized software-development model that encourages open collaboration.
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OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof.
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Path integral formulation
The path integral formulation of quantum mechanics is a description of quantum theory that generalizes the action principle of classical mechanics.
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Protein
Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.
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Software
Computer software, or simply software, is a generic term that refers to a collection of data or computer instructions that tell the computer how to work, in contrast to the physical hardware from which the system is built, that actually performs the work.
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Solution
In chemistry, a solution is a special type of homogeneous mixture composed of two or more substances.
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Solvent
A solvent (from the Latin solvō, "loosen, untie, solve") is a substance that dissolves a solute (a chemically distinct liquid, solid or gas), resulting in a solution.
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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 (trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, development starting 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 still in operation, founded in 1477.
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Van der Waals force
In molecular physics, the van der Waals forces, named after Dutch scientist Johannes Diderik van der Waals, are distance-dependent interactions between atoms or molecules.
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X86
x86 is a family of backward-compatible instruction set architectures based on the Intel 8086 CPU and its Intel 8088 variant.
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X86-64
x86-64 (also known as x64, x86_64, AMD64 and Intel 64) is the 64-bit version of the x86 instruction set.
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YASARA
Yet Another Scientific Artificial Reality Application (YASARA) is a computer program for molecular visualising, modelling, and dynamics.
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References
[1] https://en.wikipedia.org/wiki/Q_(software)
