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

[Justin A. Lemkul]

Justin A. Lemkul wrote:

<snip>

>> NOTE 2 [file em.mdp, line unknown]:
>>   You are using a plain Coulomb cut-off, which might produce artifacts.
>>   You might want to consider using PME electrostatics.

I also just noticed that you have not specified "periodic_molecules = yes" in 
the .mdp file.  This is certainly problematic, as your CNT will experience 
extreme repulsion at the box edges.

I also remembered something else to consider: in x2top from version 3.3.3, the 
-pbc option was functional.  You could perhaps use this version to create your 
initial topology to avoid all the manipulation after the fact.

-Justin

-- 
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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

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