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.
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 INDIA On Thu, Jul 30, 2009 at 5:56 PM, Vitaly V. Chaban <vvcha...@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. > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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