Software
MOLDEN
Software name:
MOLDEN
Policy
MOLDEN is freely available to users at HPC2N, however you are encouraged to register on the User Registration Form, found on the Molden page, since it will help to keep up the support for Molden.
General
MOLDEN is a general molecular and electronic structure processing program.
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.
It can also 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. Molden also features an stand alone forcefield program ambfor, which can optimise geometries with the combined Amber (protein) and GAFF (small molecules) force fields. Atom typing can be done automatically and interactively from within Molden, as well as firing optimisation jobs. Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides.
Availability
On HPC2N we have MOLDEN available as a module on Kebnekaise.
Usage at HPC2N
Since molden uses graphics, it is importantant that you log in with
ssh -Y username@host
to set the display correctly.
To use the molden module, first add it to your environment. Use:
module spider molden
to see which versions are available and how to load the module and the needed prerequisites.
Example, loading molden version 5.7
ml icc/2017.1.132-GCC-6.3.0-2.27 ml impi/2017.1.132 ml Molden/5.7
You can read more about loading modules on our Accessing software with Lmod page and our Using modules (Lmod) page.
Loading the module should set all the needed environmental variables as well as the path.
You then start molden by typing
molden
Additional info
Documentation is available on the Molden page.
Using Molden with other programs than GAMESS/Gaussian/Mopac.
There are also some useful information here and here.
Referencing
G.Schaftenaar and J.H. Noordik, "Molden: a pre- and post-processing program for molecular and electronic structures", J. Comput.-Aided Mol. Design, 14 (2000) 123-134
Updated: 2024-04-17, 14:47