[gmx-users] A question on [ bonds ]

[Anton Feenstra]

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? 

These nanotubes are usually very regular, so couldn't you count out which
atoms must be bonded to which? Taking e.g. 20 carbons around a 'ring' of
the tube, you would have bonds 1-2, 2-3, ... , 19-20, 20-1 for the
first 'ring', and then something like 1-21, 3-21, 5-23, 7-23 for the bonds
to the next ring. (I'm just guessing at your actual topology, of course.)
It shouldn't be hard to write a script or small program that would spit out
the right bonded atom pairs, given a few parameters like total number of
atoms, nr of atoms in one 'ring', and perpendicular or (semi-)paralell
orientation (w/r to tube axis).


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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