Hi I just can not find a way to overlap 2 molcules in Avogadro I
actually need to overlap the same molecule prior and after a geometry
optimization
many thanks in advance Peter
Hi I just can not find a way to overlap 2 molcules in Avogadro I actually need to overlap the same molecule prior and after a geometry optimization
I usually open up two files, and copy a molecule from one to the other. If you have the same coordinate system, they will overlap exactly.
-Geoff
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/
On 10/14/2010 7:30 PM, Geoffrey Hutchison wrote:
Hi I just can not find a way to overlap 2 molcules in Avogadro I actually need to overlap the same molecule prior and after a geometry optimization
I usually open up two files, and copy a molecule from one to the other. If you have the same coordinate system, they will overlap exactly.-Geoff
.net/lists/listinfo/avogadro-discuss
This is confusing, do you say you open these up in a different program
like openoffice or word?
The problem is that the position of the molecule does not remain the
same after, for example, running a calculation in Gaussian. If I load
the log file from that into Avogadro, the molecule is positioned very
differently. I will now try VMD with RMDS, that appears to work
Many thanks Peter
On Oct 15, 2010, at 2:35 AM, Peter Schellenberg wrote:
This is confusing, do you say you open these up in a different program
like openoffice or word?
No. You can open multiple windows in Avogadro and copy and paste between them.
I will now try VMD with RMDS, that appears to work
So what you’re saying is that you’d like to see molecule alignment in Avogadro with RMSD calculations. Several people have asked and we will surely add this at somepoint soon.
-Geoff