Molecule visualization and simulation

this page focuses and tools for drawing molecules, for analysing pictures please see under Pictures and data retrieval  Most of the 3d modeling tools have also analysis functions

2d sketching and using functions

SketchEl: very simple and small program for sketching molecules and then exporting svg http://sketchel.sourceforge.net/

JChemPaint: simple java based editor but with sufficient power to make publication ready plots https://jchempaint.github.io/

Neat little program to simulate and visualize orbitals “Orbital Viewer” http://www.orbitals.com/orb/ov.htm

3d modeling: look through all, the older might be worth consideration too

Avogadro very nice and updated 3d molecule visualisation https://two.avogadro.cc

Facio is a nice opengl based software package supporting “gaussian” and “games” https://zzzfelis.sakura.ne.jp

Jamberoo-cross platform editor with output for many simulation codes really nice but not the fastest learning curve http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html

Gabedit really nice editor with simulation code export, has more features but is not so easy to use, supports infrared and other spectroscopic programs. Gabedit can Creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem. http://sites.google.com/site/allouchear/Home/gabedit

For crystalline structures this program looks promising (have not tried it) http://jp-minerals.org/vesta/en/

Stumbled over the IQmol webpage, seems to be a nice editor but have not tried it http://iqmol.org/index.html

older version (nearly all from 2004)

Orbital viewer: show and create orbitals around molecules http://www.orbitals.com/orb/ov.htm

ArgusLab: great program for setting up 3d molecules and even run gaussian and other calculations from its platform http://www.arguslab.com/

Viewmol is a molecular editor and gaussian input, it has some interesting features worth looking at http://viewmol.sourceforge.net/index.html

one package that is only semifree is the agile package, it contains also modules for simulation, the graphics module is free together with other parts, check with your needs (it supports GPU acceleration) http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html

“know it all” is a package for teaching, like is the “molecular workbench” the later is a great online tool http://www.knowitall.com/academic/welcome.asp#Features

http://mw.concord.org/modeler/index.html

to view the structural output only molecular viewers are usually enough here I recommend

jmol: http://wiki.jmol.org/index.php/Main_Page

openrasmol does a good job too: http://www.openrasmol.org/

Moldraw also shows the molecular data, additionally it can export FEFF input files, so can be used to convert structure files into feff input files http://rsc.anu.edu.au/opensource/index.php?option=com_docman&task=cat_view&gid=69&Itemid=32

openbabel: converts all dataformats in all others (like gaussian in xyz data…) http://openbabel.org/wiki/Get_Open_Babel

Simulation Codes

ORCA - modern electronic structure program http://www.freechemical.info/freeSoftware/ORCA.html

An interesting attempt to produce a Python code for quantum chemistry calculations is pycquante, it aims towards an very understandable implementation of tools and code to do calculations, if not to the fastest one: http://pyquante.sourceforge.net/

Paid: http://www.scm.com/ADF/