toby10222224 wrote:
Hi:
I have a carbon nanotube (CNT) and several carbonly groups (C=O).
Meanwhile the carbonly carbon atoms are part of the CNT. That is to say
an oxygen atom is attached to one carbon atom of the CNT to form a
carbonyl group. All the carbon atoms are supposed to be fixed, while
carbonyl carbon and oxygen atoms are supposed to have bond interactions.
I can freeze the rest carbon atoms of the CNT, but how to deal with the
carbonly atoms?
By "fixed," do you mean their positions should be invariant (i.e. freeze groups)
or that their bond lengths should be constrained? If the former, then you
should be able to make use of index groups to define an appropriate freezegrp in
the .mdp file. If the latter, use "constraints = none" in the .mdp file, and
write a [constraints] directive for the bonds you do wish to be constrained.
-Justin
Any suggestions are appreciated!
Thank you in advance!
2011-05-09
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toby10222224
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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