Author Archives: Dan Gezelter

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 … Continue reading →

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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 … Continue reading →

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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, … Continue reading →

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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 … Continue reading →

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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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