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

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 30 14:05:45 CET 2009

Cun Zhang wrote:
> hi, Justin.  Thank you for your meticulous and patient explanation !
> Before I see this post, I misunderstood the meaning of sharing bonds.
> I thought note only the bonds,but also the angles and the dihedrals
> should be added to top file.

I see now that I should have been more careful in my explanation.  It is better 
stated that *bonded parameters* should extend across periodic boundaries, not 
just bonds.  But the same principle applies.

> It was so complicated to deal manually that I wrote that script.

That's sensible, but I didn't understand what your scripting was doing with 
renumbering and all that.  Just add the appropriate parameters to the .top, 
given the numbering in the coordinate file.

> I will read the doucment you mentioned carefully .

The CNT how-to was painstakingly assembled by Chris Stiles a few years ago after 
many conversations like this one.  He has done a nice service by assembling the 
tutorial.  I believe it applies to version 3.3.3, but many of the principles are 
the same.  Remember, as I suggested before, that x2top from the 3.3.3 
distribution works with the -pbc option, which does all of the complicated work 
for you.  Not a bad option for your initial topology generation.

>  And I will fix these notes and warnings as grompp and mdrun suggest.

Good idea :)



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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