VMD-L Mailing List

From: florian.naegele_at_uni-ulm.de
Date: Thu Feb 17 2022 - 03:39:37 CST

Dear VMD team,

 

I want to visualize molecular orbitals from a molden file. In principle that works fine, but I discovered some differences in the
output produced by VMD, compared to molden or GaussView.

To me it looks like VMD has some problems with basis sets containing g functions, or with the ordering of the cartesian functions.

I took a quick look into the source code of the molden plugin, and there, everything seems fine and in line with the conventions for
the molden file format.

I'm using VMD version 1.9.4a51.

Under the following link, you can find an example, containing the Gaussian formatted checkpoint file, the molden file and the vmd
script I used to generate the picture of the orbitals, as well as

screenshots from the settings and the output in all three programs:

 

https://urldefense.com/v3/__https://cloudstore.uni-ulm.de/s/EbYbsF7k28HbP5w__;!!DZ3fjg!s1Xy7GLLk7gC5I4V9QSrxkbkau5WkDXiLndK_kfN9q4XM_GzDUsDEZLIEOtAEcUdvg$

 

The example is a chemical not meaningful MoO molecule, but it shows nicely the problem I also found with 'real' molecules.

I chose the beta MO number 13, because with this, the difference between the VMD output and the other two programs is very
prominent.

 

I generated the molden file from the Gaussian .fchk file with the help of 'multiwfn', to convert the spherical harmonics to a
cartesian basis set, and first thought, that something in this conversion went wrong,

but the output from molden with the .molden file in cartesian basis is identical to the output from Gaussview, using the .fchk file
which contains the spherical basis set.

 

To visualize the orbitals, I could of course also use cube files from Gaussian, but in my opinion, this has some disadvantages
compared to using the molden file directly in VMD:

Cube files need a lot of diskspace and also quite some time to calculate them, and even high-resolution cube files don't give such a
smooth and nice output that VMD can render from the molden file.

 

I would really appreciate if you could have a look into the problem with the molden files.

 

Thanks in advance and kind regards

Florian