Hi,<br><br>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.<br>
<br>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)).<br>
<br>With regards,<br><br clear="all">Manik Mayur<br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>INDIA<br>
<br><br><div class="gmail_quote">On Thu, Jul 30, 2009 at 5:56 PM, Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
If you unzipped/untarred the archive properly it should be some system<br>
already prepared to run. So you can just start grompp and mdrun to<br>
begin MD.<br>
<br>
<br>
><br>
> 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.<br>
><br>
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