Molden

The Molden software can be used for visualizing geometries and molecular orbitals.

It can read GAMESS and GAUSSIAN output files and some other formats, including xyz files and PDB files.  

For more information, see links below.  

MOLDEN ON STALLO

Current version: OpenGL version of Molden 4.6

To run molden on stallo, load the module:

$ module load molden

Then call molden:

$ gmolden

TIP: If you want to avoid to have to load the module for every use, add the module load molden command to your .bash_profile or .profile file.

SOME GUIDELINES ON USE 

Reading Gaussian outputfiles:

Molden can read and animate geometry optimizations from Gaussian outputfiles. If you want to read information on molecular orbitals also, you need to add these keywords to the gaussian input file in the route section: 

#P GFINPUT IOP(6/7=3)

Reading XYZ files:

To read xyz coordinate files with molden, the format has to be as follows:

Example:
------------------------------------------------------
3
                                                                      Blank line!
O       0.000000    0.000000    0.047929
H       0.000000   -0.813054    0.619662
H       0.000000    0.813054    0.619662  
------------------------------------------------------

LINKS

General information and guidelines on use:

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