[gmx-users] Carbon Nanotube Simulations
bobjohnson1981 at gmail.com
Thu Mar 29 17:04:04 CEST 2007
Do you want to simulate an infinite nanotube or a finite one?
On 3/28/07, George Abadir <georgea at ece.ubc.ca> wrote:
> There is no C1 and C2 atom in the input PDB file, and the topology file
> is not generated because x2top doesn't generate a topology because of
> the errors. I don't understand what C (1) and C (2) means but it is not
> C1 and C2; I mean not two different types of atoms. The PDB file is
> generated simply from tubegen and I defined the residue type in the rtp
> Mark Abraham wrote:
> > George Abadir wrote:
> >> Hi, thank you very much for your help.
> >> I capped the CNT with hydrogen atoms (i.e., I changed the carbon
> >> atoms at the ends of the tube into hydrogen atoms), but now I get an
> >> error "No
> >> forcefield type for atom C(1) with 2 bonds" instead of ""No
> >> forcefield type for atom C(2) with 1 bonds" ! Is there any way to
> >> solve this?
> > Not without knowing what's wrong with the topology for C1 and C2.
> > That's your job :-)
> > Mark
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