[gmx-users] A question on [ bonds ]

[Daan van Aalten]

Dear Zhangwei

Would you be able to provide a PDB file of your nanotube - we'd like to
try it with a "large" version of the PRODRG program here.

cheers

Daan



On Thu, 14 Aug 2003, zhangwei wrote:

> Hi,all
>    I want to simulate a carbon nanotube. If the harmonic bond streching is used to simulate the C-C interation interlayer, how could I write the [ bonds ] directive? Should I find neighbors of every carbon atom, and list them in the [ bonds ] directive? It'll be hard to do it. I didn't find x2top helpful to write the topology of a carbon nanotube.  And is the [ bonds ] directive indispensable?
>    Incidentally, thanks for Anton's answer.
>
> ¡¡¡¡¡¡
>
>
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Wei Zhang
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡zhangw at sinr.ac.cn
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2003-08-14
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
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