Molden

Please note that this application page is referring to the old CentOS software stack which is obsolete and does not work any more with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page.

Category

Visualization, Chemistry

Description

Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. Both Xwindows and OpenGL versions of Molden are also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. Molden also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
		5.6

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
5.6	module load new gcc/4.8.2 molden/5.6

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Interactive session

In order to start an interactive Molden session on one of the login nodes, you need to login to the Euler cluster with X11 forwarding enabled. After loading the required modules

module load new gcc/4.8.2 molden/5.6

you can start Molden with the command molden.

Molden GUI, please click on the picture to see a larger version

Example

Molden example, please click on the picture to see a larger version

License information

copyright for non-commercial use

Links

http://www.cmbi.ru.nl/molden

https://en.wikipedia.org/wiki/Molden
http://www.cmbi.ru.nl/molden/CopyRight.html