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Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 1990s.
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The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.
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Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.
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Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
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In computer software, Orac is a classical molecular dynamics program, to simulate complex molecular systems at the atomistic level. In 1989-1990, the code was written originally by Massimo Marchi during his stay at International Business Machines (IBM), Kingston (USA). In 1995, the code was developed further at the Centre européen de calcul atomique et moléculaire (CECAM). It is written in the programming language Fortran. In 1997, it was released under a GNU General Public License (GPL). The latest release of Orac may be run in parallel using the standard Message Passing Interface (MPI) libraries, allowing replica exchange simulations, multiple walkers metadynamics simulations and multiple steered molecular dynamics nonequilibrium trajectories.
Qbox is an open-source software package for atomic-scale simulations of molecules, liquids and solids. It implements first principles molecular dynamics, a simulation method in which inter-atomic forces are derived from quantum mechanics. Qbox is released under a GNU General Public License (GPL) with documentation provided at http://qboxcode.org. It is available as a FreeBSD port.
References
- ↑ Toukan K & Rahman A (1985). "Molecular-dynamics study of atomic motions in water". Physical Review B. 31 (5): 2643–2648. Bibcode:1985PhRvB..31.2643T. doi:10.1103/PhysRevB.31.2643. PMID 9936106.
- ↑ Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). "Semianalytical treatment of solvation for molecular mechanics and dynamics". J Am Chem Soc. 112 (16): 6127–6129. doi:10.1021/ja00172a038.
- ↑ Tinker license