GAMESS

Posted on February 23, 2001 by Dan Gezelter

The General Atomic and Molecular Electronic Structure System is a freely availible general ab initio quantum chemistry package. Free graphics programs are also availible for downloading.
Find GAMESS at: http://www.msg.ameslab.gov/GAMESS/GAMESS.html

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Moldy

Posted on February 23, 2001 by Dan Gezelter

MOLDY is a parallelised OpenMP short-ranged molecular dynamics program, first written at Harwell Laboratory in the 1980s. The program is rewritten in a modular fashion to allow for easy user modification, in particular the implementation of new interatomic potentials. Using Link Cells and Neighbour Lists, the code fully exploits the short range of the potentials, and the slow diffusion expected for solid systems.

The code allows for a wide variety of boundary conditions, including constant pressure, temperature and strain rate. It also incorporates molecular statics via the conjugate gradients minimisation of the enthalpy.

The code will enable simulation of millions of atoms using short range potentials. Currently modules for Embedded Atom, Finnis-Sinclair, Lennard Jones and Morse potentials exist. In addition, the “magnetic” potential formalism of Ackland and Wallenius is available for separate compilation. Alloys containing a number of elements can be simulated, subject only to the available potentials.
Find Moldy at: https://code.google.com/p/moldy/

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EMBOSS

Posted on February 23, 2001 by Dan Gezelter

EMBOSS is “The European Molecular Biology Open Software Suite”. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

Find EMBOSS at: http://emboss.sourceforge.net/

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Kemistry

Posted on February 23, 2001 by Dan Gezelter

KDE-inspired molecular weight calculator
Find Kemistry at: http://kemistry.sourceforge.net/

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MOPAC7

Posted on February 23, 2001 by Dan Gezelter

MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
Find MOPAC7 at: http://www.ccl.net/cca/software/LINUX/mopac7/index.shtml

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qmol

Posted on February 23, 2001 by Dan Gezelter

qmol is a simple molecular weight calculator. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %).

Find qmol at: https://sourceforge.net/p/qmol/wiki/Home/

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The Gri graphing language

Posted on February 23, 2001 by Dan Gezelter

Gri is an extensible plotting language for producing scientific graphs, such as x-y plots, contour plots, and image plots. It was written by a scientist and therefore has the sorts of things a scientist needs. It is much like LaTeX, in that it rewards u
Find The Gri graphing language at: http://www.phys.ocean.dal.ca/~kelley/gri/

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Fungimol

Posted on February 23, 2001 by Dan Gezelter

Fungimol is an extensible system for designing atomic-scale objects. The intent is to eventually extend it to be a useful system for doing molecular nanotechnology design work. At the moment it’s a PDB file viewer and Buckminsterfullerine editor.

Find Fungimol at: http://www.fungible.com/fungimol/

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The Brenner Potential

Posted on February 23, 2001 by Dan Gezelter

C code for Brenner Potential Molecular Dynamics
Find The Brenner Potential at: http://www.rahul.net/pcm/brenner/

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NCO

Posted on February 23, 2001 by Dan Gezelter

Tools for manipulating netCDF data files
Find NCO at: http://nco.sourceforge.net/

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