[gmx-users] A question on [ bonds ]

David spoel at xray.bmc.uu.se
Sun Aug 17 11:44:00 CEST 2003

On Thu, 2003-08-14 at 15:40, 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.
x2top should work, but you may have to edit the .n2t file slightly.
Furthermore you have to select the right forcefield (only one
supported). I don't know whether the impropers will be OK though.

If prodrg works, thats probably more accurate.

>         Wei Zhang
>         zhangw at sinr.ac.cn
>           2003-08-14
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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