Daily Archives: August 3, 2010

Some software trickery…


This post will become updated continuously in order to include as much of these useful tips as I find along the way, so if you are interested please subscribe so you don’t have to visit often. Some are old or even a bit obsolete in terms of software versions but I still include them so they can all be gathered in one place; this is basically a summary of some common errors in the use of Gaussian (G03 and G09). Please feel free to comment on this post, sharing your tricks with various programs in whatever branch of computational chemistry you might be working on.

Vibrations calculated with Gaussian 09 can’t be visualized with GaussView 3.x

*Change the lines “Atom  AN” with “Atom AN”. They look the same but there are TWO spaces in the first (this is the way G09 prints the output files) and in the second one there is only ONE space. The credit is entirely due to Jean Poully who posted this trick on the CCL a few months ago.

*Reader John Keller from Alaska suggests to use the formatted chk file (.fchk) to avoid this problem. As usual with formatted chk files make sure you format them in the same computer where you calculated it, or at least make sure both versions are compiled under the same architecture (32 or 64 bits).

Molecules appear flat on Molekel versions previous to 5.x

Molekel 4.x reads Gaussian98 files only. Gaussian03 and Gaussian09 files need to have the header corrected in the following part, right at the beginning of the file:

******************************************
Gaussian 09:  EM64L-G09RevA.02 11-Jun-2009
9-May-2010
******************************************

Change to:

******************************************
Gaussian 98:  EM64L-G09RevA.02 11-Jun-2009
9-May-2010
******************************************

A rather old one and kind of a weird one too but it works and some of us (myself very much included) like the previous Molekel far more than the new 5.x version.

Electrostatic potentials can not be visualized with Molekel 4.x

This is an error that stems from the fact that atomic charges are not read by Molekel, so all electrostatic properties derived from them are not calculated nor visualized. The problem is that Gaussian also changed the header for the charges when going from Gaussian98 to Gaussian03. In Gaussian 98 charges are labeled as “Total Atomic Charges”. In G03 and G09, atomic charges are labeled “Mulliken Atomic Charges”. Therefore find and change this label for the latter. PLEASE NOTE that Molekel will look for the title “Total Atomic Charges” so if your calculation was a geometry optimization then you have to find the set of charges that correspond to the last step of it. Look for the last string and change that one; you may also change them all with the right edition option in your editor, Molekel will use the last one since that should be the one corresponding to the optimized structure.

jbf

I’ll post something else when I find/remember it. Thanks for reading!

Mi amor!!!
Muchísimas felicidades!!! Estoy muy orgulloso de ti, de ser tu novio y tenerte en mi vida. Como persona y como profesional no eres más que admirable. Al igual que quienes te escriben, estoy seguro que este es solo el principio, mi amor, ese negocio en tus manos va a llegar hasta donde tu papá siempre quiso y aun más lejos. Te amo y estoy
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