MOLDEN¶

MOLDEN is a pre- and post processing program of molecular and electronic structure.

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.

Gijs Schaftenaar, Elias Vlieg and Gerrit Vriend,”Molden 2.0: quantum chemistry meets proteins”,
J Comput Aided Mol Des (2017) 31: 789

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 

Overview¶

MOLDEN is a general molecular and electronic structure processing program.

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.

Usage at HPC2N¶

On HPC2N we have MOLDEN available as a module.

Loading¶

To use the Molden module, add it to your environment. You can find versions with

module spider Molden

and then you can find how to load a specific version (including prerequisites) with

module spider Molden/<version>

Example, loading Molden version 6.8¶

module load GCC/9.3.0
module load Molden/6.8 

Loading the module should set all the needed environmental variables as well as the path.

Running¶

After loading the module, you can start Molden by typing:

molden

Additional info¶

• Documentation is available on the Molden page.
• Using Molden with Gaussian.
• Using Molden with MOPAC.
• Using Molden with other programs than GAMESS/Gaussian/Mopac.