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

[Justin A. Lemkul]

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 
severely.

> 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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================