Faculty for Chemistry and Pharmacy - Group of Prof. Zipse
 

Molden

The program Molden by Gijs Schaftenaar at the Centre for Molecular and Biomolecular Informatics is a very nice program to visualize the results of quantum chemical calculations. In contrast to GaussView Molden reads a number of different input and output file formats, including those of Gaussian 98 and Gaussian 03. In order to start Molden type:

molden &

on the command line. All program options can be accessed through the Molden Control panel. In order to open a file, push the Read button and select the file from the popup window. In some cases (more than 512 files in the directory) Molden might not display all files contained in a directory. Upon loading a file, Molden will display the first structure encountered in this file. For geometry optimizations, this usually is the UNOPTIMIZED structure. All other structures contained in the file can be obtained with the Next button and all structures can be viewed in sequence by choosing Movie. Using the command:

molden test1.log &

it is also possible to load the file "test1.log" automatically after the program has started. New files can be generated through pushing the Write button and supplying a file name.

Display options are set with the buttons listed under "Draw Mode:", their meaning being selfexplanatory in most cases. The absolute size of the display and the position of the molecule(s) in the drawing window can be adjusted with the options gathered next to the "Zoom:" label.

Several possibilities exist for moving the molecule around on the screen. Simple horizontal or vertical translations can be affected using the arrow buttons in the lower right of the Molden Control panel. The molecule can be rotated in an "Old Style" or in a "Sticky Pointer" fashion. Selection of the mode of rotation is made through the small button in the lower right corner of the Molden Control panel. The stepsize in the "Old Style" mode is controlled through the circular button in the middle of the arrow keys of the Molden Control panel.

The three buttons under the "Calculate:" label can be used to measure distances, bond angles and dihedral angles in the structure currently on display. Of particular value is the distance measurement, that can be used to monitor the development of a bond distance along a reaction pathway or other sequence of multiple structures (Choose Monitor from the Molden Calculate panel).

A very useful tool for following geometry optimizations can be found under "Geom. conv." under the Convergence label, which produces a graphical display of the most important parameters during a geometry optimization (total energies, step sizes, forces).

In order to stop Molden, push the button with the pirat flag on top.

In case nothing works: on startup Molden generates a file called "plot". This requires the permission to write in that specific directory. Users therefore cannot usually start Molden from directories of other users or system-wide importance.

An updated version of Molden (version 4.2) can be started using the command molden42.
 


last changes: 06.11.2007, HZ
questions & comments to: zipse@cup.uni-muenchen.de