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

Manik Mayur manik.mayur at gmail.com
Thu Jul 30 21:40:34 CEST 2009


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

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)).

With regards,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur

On Thu, Jul 30, 2009 at 5:56 PM, Vitaly V. Chaban <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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