To anyone who can help,
I have been trying to apply constraints, angles and bond distances from
a neutron diffraction study, to a simple ammonia borane molecule
(NH3BH3). I apply constraints by going to: (extensions->molecular
mechanics->constraints) which opens the constraints table. After
inputting the constraint parameters the structure will not update and
herein lies the problem. I want to be able to export an Nwchem file with
the exact applied constraints. If I preform a simple optimization in
Avogadro, before exporting to nwchem, the constraints are used, but the
bond angles and distances are not the exact parameters I require. Is
there a why to render or apply the exact constraints before exporting?
I’ve attached the file I’m trying to constrain as well as a png image of
the constraints used. Any help would be greatly appreciated.
-Richard
P.S. My system specs are as follows:
Ubuntu 11.10 x64
Avogadro version 1.0.3 (installed with apt-get)
Library version 1.0.3
Openbabel version 2.3.0
Qt version 4.7.3
Hi Richard,
The constraints may not be exact because the optimizer will slowly apply them. There’s also a penalty function for “breaking” constraint – depending on the energetics of the system, you might get slightly “off” values.
If you need the exact angles and distances, you can do that through the Bond and Angle property windows. Go to View->Properties->Bond Properties. You can click on the distances and type a number to edit the distance. Same thing goes for View->Properties->Angle Properties for angles.
Hope that helps,
-Geoff
On Dec 7, 2012, at 7:33 PM, Richard Overstreet reoverstreet1@catamount.wcu.edu wrote:
To anyone who can help,
I have been trying to apply constraints, angles and bond distances from a neutron diffraction study, to a simple ammonia borane molecule (NH3BH3). I apply constraints by going to: (extensions->molecular mechanics->constraints) which opens the constraints table. After inputting the constraint parameters the structure will not update and herein lies the problem. I want to be able to export an Nwchem file with the exact applied constraints. If I preform a simple optimization in Avogadro, before exporting to nwchem, the constraints are used, but the bond angles and distances are not the exact parameters I require. Is there a why to render or apply the exact constraints before exporting? I’ve attached the file I’m trying to constrain as well as a png image of the constraints used. Any help would be greatly appreciated.
-Richard
P.S. My system specs are as follows:
Ubuntu 11.10 x64
Avogadro version 1.0.3 (installed with apt-get)
Library version 1.0.3
Openbabel version 2.3.0
Qt version 4.7.3
<12042012NH3BH3.xyz><Screenshot at 2012-12-06 16:56:10.png>------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d_______________________________________________
Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options