[gmx-users] Re: R: R: R: CNT

[Justin A. Lemkul]

Manik Mayur wrote:
> Hi,
> 
> Since in graphene, C is sp2 hybridized with covalent radius as 0.073 nm, 
> how come C-C bond length =0.142 nm which is less that twice the covalent 
> radius, does this mean 2 C's overlap (which is unphysical). The source 
> of my data is wikipedia.
> 

Wikipedia will also tell you that a bond formed between two atoms is *not* 
purely the sum of their covalent radii: "In principle, the sum of the two 
covalent radii should equal the covalent bond length between two atoms. This 
relationship does not hold exactly because the size of an atom is not constant 
but depends on its chemical environment."

http://en.wikipedia.org/wiki/Covalent_radius

That said, Wikipedia is not the be-all end-all for truthful information.  Data 
from the literature and chemical texts is often more reliable :)

> Also, there is no bare C in GROMOS96 53a6 ff, which has LJ parameters 
> for a sp2 C, though I could find CH0, which is for sp3 C. Can somebody 
> please suggest from where should I get LJ parameters for sp2 C? From the 
> tutorials I found that bare C is used in topologies, which according to 
> my calculations has VdW radius = 0.179 nm (0.5*(C12/C6)^(1/6)).

There is a "bare carbon" in 53a6, it's atom type C (from the .atp file), i.e. 
aromatic sidechains.

-Justin

> 
> With regards,
> 
> Manik Mayur
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
> INDIA
> 
> 
> On Thu, Jul 30, 2009 at 5:56 PM, Vitaly V. Chaban <vvchaban at gmail.com 
> <mailto:vvchaban at gmail.com>> wrote:
> 
>     If you unzipped/untarred the archive properly it should be some system
>     already prepared to run. So you can just start grompp and mdrun to
>     begin MD.
> 
> 
>      >
>      > By the way, I had already seen that web page... I downloaded and
>     unzipped the swcnt file, but I can't understand what kind of file it is.
>      >
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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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