Molecule visualization and simulation

Posted on Sun 26 June 2022 in Scientific software/Molecule

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

JChemPaint: simple java based editor but with sufficient power to make publication ready plots

Neat little program to simulate and visualize orbitals “Orbital Viewer”

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

Avogadro very nice and updated 3d molecule visualisation

Facio is a nice opengl based software package supporting “gaussian” and “games”

Jamberoo-cross platform editor with output for many simulation codes really nice but not the fastest learning curve

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.

For crystalline structures this program looks promising (have not tried it)

Stumbled over the IQmol webpage, seems to be a nice editor but have not tried it

older version (nearly all from 2004)

Orbital viewer: show and create orbitals around molecules

ArgusLab: great program for setting up 3d molecules and even run gaussian and other calculations from its platform

Viewmol is a molecular editor and gaussian input, it has some interesting features worth looking at

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)

“know it all” is a package for teaching, like is the “molecular workbench” the later is a great online tool

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


openrasmol does a good job too:

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

openbabel: converts all dataformats in all others (like gaussian in xyz data…)

Simulation Codes

ORCA - modern electronic structure program

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: