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

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 25 04:07:43 CET 2009

Justin A. Lemkul wrote:


>> 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 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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