Wednesday, June 3, 2009


My first screencast! OK, actually it is my 3rd. The first one was a movie of my cursor moving around on the screen (I'm saving that for the bloopers reel), and in the second (my first real attempt) I forgot to move a window. The fact that I got this on the 3rd try tells you something about how easy it is to do this (though adding the comments takes a little time).

Anyway, this screencast gives a very brief overview of molecule-building with Avogadro and setting up a GAMESS input file.


Rich Apodaca said...

Jan, a series of screencasts on using molecular modelling software sounds like a great idea.

Although the subject material is completely different, Railscasts may be a site you could draw some inspiration from. At the very least, it might be interesting to play around with the sofware that's used.

Jan Jensen said...

Jacob Lerche from Portland State University writes

Hi Jan, I hope you don't mind me asking you a couple questions. I
recently started reading your blog because I became interested in the
possibilities of molecular modeling. I wanted to ask if you've been able to load a GAMESS output file into Avogadro and successfully
generate electrostatic potential maps, MOs, or other such things. I am seemingly able to do so with MacMolPlt, but I have yet been able to do
it in Avogadro. The other question is if you would be willing to
explain to me how to access GAMESS from the command line. I've had to
resort to using the bundled queuing program, gamessq, which might be
the basis for my troubles.

Thanks for your time, I'm looking forward to hearing from you.


Jan Jensen said...

Glad to hear it!

Unfortunately Avogadro is not yet able to extract the required information from the GAMESS output file. I use MacMolPlt.

I use the gms script that comes with GAMESS: "./gms xxx" where xxx is the input file xxx.inp.
You have to be in the gamess directory for this to work.

Craig Blain said...

Whenever I try the precompiled GAMESS on my MacBook with OS X 10.4 I get the following error from any GAMESS script, even the included examples:

unset echo
.//ddikick.x .//gamess.Jan122009R3.x ../../../Users/Craig/.gamessqd/exam01_1 -ddi 1 1 localhost -scr ./
Bus error
unset echo

Other people have had this problem, but I haven't heard of a solution. Have you encountered this before?