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How can I do the most accurate geometry optimization on Ubuntu?

Asked by [ Admin ]

I know of the various chemistry tools available on Ubuntu and Debian, but was wondering how I can calculate the most accurate (i.e. using the most accurate method) geometries? I am not worries about conformations; that would be a mere extra. I like to start with an XYZ or MDL molfile I created with Jmol, so the method should start there.

OpenBabel can likely apply the UFF force field, but Jmol shares that code. What can I do beyond force fields? How would I set up the appropriate input and run the calculation? Limitations: software must be installable from Ubuntu repositories.

NN comments
steve wathen
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Is Geometry the only thing you are interested in, or do you need an accurate energy term like Heat of Formation? For geometry, Force fields are pretty reliable for most organic compounds unless your molecule is unusual.

chem-bla-ics
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wathen Geometry, when I wrote up this one. I guess it’s part of the question what is most reliable for unusual molecules, and what is unusual.

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4 answers

1

steve wathen [ Editor ]

Avogadro can be used to generate input files for a number of other computational packages – the only one I have experience with is Mopac.  If you have Mopac 2009 installed, you can submit directly to Mopac from within Avogadro and then view the results.  


In Avogadro:  Build your molecule, go to the Extensions menu and select MOPAC … save the file and click Compute …  The result should then be automatically displayed in Avogadro.
NN comments
chem-bla-ics
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Mopac2009 is not packaged for Ubuntu; is it supposed to work with Mopac7 too? I guess not, because the MOPAC dialog only has a Generate button, and not the Compute button… :(

steve wathen
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You should be able to run Mopac7 from the command line. Use Avogadro to generate the .mop input file using the AM1 or PM3 method. The default PM6 method isn’t available in Mopac7.

Assuming that you have mopac in the PATH, At the command line type: mopac myFile.mop The results will be in: myFile.out Avogadro can open the .out file

If you would rather do it all at the command line, you should be able to use OpenBabel to generate the .mop file and convert the output file into something that Jmol can open. Then you can skip using Avogadro.

chem-bla-ics
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1: can you integrate your last comment with the main answer? 2: it’s been a long while since I studied QM and semi-empirical methods… AM1 or PM3: which can I expect to give better energy value predictions? Any literature I should read up on?

chem-bla-ics
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Mmmm… Avogadro is not able to create a PM3 file compatible with Mopac7 on Ubuntu :( Will try OpenBabel then…

steve wathen
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-bla-ics That’s odd, I would have thought there would not be that much difference between the two versions of Mopac. Avogadro includes the keyword AUX – maybe AUX is new to Mopac 2009 – try editing the .mop file and deleting the AUX keyword.

steve wathen
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-bla-ics In general, I think that PM3 is probably a little better than AM1 but I’m not an expert. Amides can be funny, you need to add the keyword MMOK for the amide geometry to optimize correctly.

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0

kml [ Editor ]

Avogadro can also do force fields, and it may be easier for a GUI-oriented user. Beyond force fields, any of the programs that do quantum-based structure optimization are  options…. MPQC, psi3, ABINIT. I don’t know of any good GUIs for preparing input for them, though. I noticed gabedit, but I haven’t used that so I can’t recommend it.

NN comments
chem-bla-ics
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Can you explain how to do it? I have it installed, see the various tools for geometry optimization, and some have a ‘Compute’ button… but nothing really happens. How do I get Avagadro to use Mopac or MPQC which I have both installed already?

kml
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-bla-ics If you’re asking about gabedit, I don’t know. As far as Avogadro is concerned, it only does molecular mechanics (I think), but there is a MOPAC input generator (

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0

alfonsnic

You can also user the libraries of Dynamo for Python, pDynamo http://www.pdynamo.org/mainpages/

Is has lots of classes to optimize molecules, perform molecular dynamics,…

NN comments
alfonsnic
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-bla-ics As far as I know, there is no Ubuntu package for it. You have to download the libraries and manage as a normal Python libraries. In the file you download, there are several examples.

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