[gmx-users] Carbon Nanotube Simulations

[George Abadir]

I finally managed to cap it with hydrogen and I don't get any errors 
now. It seems I had a wrong bond-length at the beginning. Thanks guys 
for your your help :)
George

Robert Johnson wrote:

> Do you want to simulate an infinite nanotube or a finite one?
> Bob
>
> 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
>> file.
>> Thanks
>>
>> 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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>>
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