[gmx-users] A question on [ bonds ]
spoel at xray.bmc.uu.se
Sun Aug 17 11:44:00 CEST 2003
On Thu, 2003-08-14 at 15:40, zhangwei wrote:
> 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
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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