[gmx-users] How to make carbon nanotube infinite?

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 19 15:09:39 CET 2009

Cun Zhang wrote:
> Hi,gmx users,
> I want to set CNT infinite in the system of CNT and water.  I'm using 
> GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file.

Not possible, Gromacs 4.1 hasn't been released :)  If you're using version 
4.0.1, you shouldn't, because it has a nasty bug that affects performance very 

> I set the box size larger than CNT's length a C-C bond(half up and half 
> down).
>  If I don't do a EM, it will crumble. But if I do it,it can't satisfy 
> that the box size is larger then CN't length a C-C bond.

I don't understand this.  Are you getting any error messages?  Screen and log 
output are more useful in most cases.

> I have searched google and gmx mail list, but still can't solve it .
> I found that GMX online document about Carbon 
> Nanotube(http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube)
> say,
> Be absolutely sure that the "terminal" carbon atoms are sharing a bond 
> in the topology file.
> I don't understand it.How should I do?

Make sure there is a bond in your topology between the appropriate atoms at one 
"edge" of the box to the appropriate atoms at the other "edge" of the box.



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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