[gmx-users] rigid linear molecules

[Anton Feenstra]

Gianfranco Bocchinfuso wrote:
> if I have a linear molecule A--B--C what is the problem if I use shake to
> constrain the bonds A-B, B-C and A-C? I think that the 3rd constrain make
> the molecule linear, or not?

No, within even a small tolerance (e.g. shake_tol, or the tolerance resulting
from a certain lincs_order) for the bond lengths, there is a considerable
freedom for the atoms to be out of line. It's basic trigonometry -- work it
out if you like.


-- 
Groetjes,

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