OpenScience / Software / Chemistry



XMD

Posted on August 2, 2006 by Dan Gezelter

XMD is a GPL’ed Molecular Dynamics program written in C. It supports the following potentials: pair, EAM, Tersoff and Stillinger-Weber, and implements a large variety of commands to help simplify simulation. Find XMD at: http://xmd.sf.net

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Posted in Molecular Dynamics | Leave a comment

iBabel cheminformatics and molecule viewer

Posted on July 5, 2006 by Dan Gezelter

This is an Applescript Studio application that provides a front-end for a variety of Cheminformatics tools. To date these include file conversion (between a vast range of chemical file formats), SMARTS-based substructure searching, similarity searching, list manipulation, overlaying using OpenBabel, … Continue reading →

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Posted in Molecule Viewers and Editors | Leave a comment

The CCP1GUI

Posted on May 26, 2006 by Dan Gezelter

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes. Find The CCP1GUI at: http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/

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JSpecView

Posted on March 11, 2006 by Dan Gezelter

JSpecView is a viewer for spectral data in the JCAMP-DX format. Find JSpecView at: http://jspecview.sourceforge.net/

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Posted in Spectroscopy | Leave a comment

VMD

Posted on February 13, 2006 by Dan Gezelter

Useful for viewing PDB files, etc. Relatively powerful configuration for graphical representation of molecule. Find VMD at: http://www.ks.uiuc.edu/Research/vmd/

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BKchem

Posted on January 24, 2006 by Dan Gezelter

BKchem is free chemical drawing program with many features, written in python. Find BKchem at: http://bkchem.zirael.org/

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Posted in Molecule Viewers and Editors | Leave a comment

V_Sim

Posted on October 12, 2005 by Dan Gezelter

V_Sim visualizes atomic structures such as crystals, grain boundaries, etc. V_Sim can use information from files in binary d3 format, in ascii, or in "xyz" format. Find V_Sim at: http://www-drfmc.cea.fr/sp2m/L_Sim/V_Sim/index.en.html

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PGOPHER

Posted on July 26, 2005 by Dan Gezelter

PGOPHER is a general purpose program for simulating and fitting rotational spectra. PGOPHER will handle linear molecules and symmetric and asymmetric tops, including effects due to unpaired electrons and nuclear spin. The program can handle many sorts of transitions, including … Continue reading →

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Posted in Spectroscopy | Leave a comment

Zori

Posted on May 3, 2005 by Dan Gezelter

Zori is an open-source quantum monte carlo package for the electronic structure of atoms and molecules. Find Zori at: http://www.zori-code.com

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Posted in Ab Initio Quantum Chemistry | Leave a comment

MayaChemTools

Posted on April 21, 2005 by Dan Gezelter

MayaChemTools provides a variety of scripts – some straightforward and others a bit more involved – to work with SD files, CSV/TSV text files, and databases: splitting, joining, merging, and sorting SD and text files; merging text files into SD … Continue reading →

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Posted in Chemical Information | Leave a comment