[gmx-users] a mess result

[Anton Feenstra]

Wei Zhang wrote:
> Hi,all
> 
>    I'm simulating a carbon nanotube. I use bond and angle harmonic
> potential for the bonding of carbon atoms. When pbc=no, it gives good
> result. But when I used periodic boundary condition, the result
> structure is a mess. Why? Could you help me?

Does your nanotube stretch across the pbc, i.e. is it in itself periodic?
In that case you may need the GMXFULLPBC option (setenv GMXFULLPBC 1).


-- 
Groetjes,

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