[gmx-users] freeze the carbonyl carbon atoms

Justin A. Lemkul jalemkul at vt.edu
Mon May 9 12:58:04 CEST 2011

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.


> Any suggestions are appreciated!
> Thank you in advance!
> 2011-05-09
> ------------------------------------------------------------------------
> toby10222224


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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