trying to use "extended molecule"

31 views
Skip to first unread message

Chitrak

unread,
Mar 22, 2013, 8:01:43 PM3/22/13
to spinev-...@googlegroups.com
Hi everyone,

I was looking at the "tppmchn" example where an "extended molecule" has been used. Is it usable only if one of the nuclei is 1H? I get an error "unknwon nucleus" when I try to change this nucleus.

Related to that, I am basically trying to simulate the ROCSA experiment [Chand and Tycko, J. Chem. Phys., 118, 8378 (2003)]. I am trying to figure out how to define the carbonyl CSA orientation. I feel the easiest way would be to define an extended molecule (by including the carbonyl oxygen) and define it with respect to the plane formed by the bonds. Is there any other way by which I could do this?

Chitrak.

Mikhail Veshtort

unread,
Mar 23, 2013, 4:53:46 PM3/23/13
to spinev-...@googlegroups.com
Hi Chitrak,

The extended molecule functionality works for any nuclei. You probably get the "unknown nucleus" error because you replaced H1 with some other nucleus at the "nuclei" line, but left it at the "options" line (in the -sysch$N option). This combination is indeed meaningless.

Regarding the other question, you are on the right track. For an example of how you can set up fragments of large complex molecules (including the CSA tensors) for simlutations in SpinEvolution, check out the pdsd example. Or just read the sections of the Manual concerning the Extended molecule, Local coordinate systems, and sys2ext_map variable. Depending on how you will be setting up your extended molecule, you may also find useful explanations in the Construction of the molecule section.

Best regards,
Mikhail
Reply all
Reply to author
Forward
0 new messages