[gmx-users] rigid linear molecules

[Anton Feenstra]

lulanyuan wrote:
> Thanks for reply. But after reading the whole discussion of acetonitril, I found that to ajust the moment
> of inertia, I have to change the bond length. I think this totally changed the model and will affect the other
> parameters in the model(charges and LJ).
> Does anyone do things like this kind of mass redistribution in literature? Can anyone
> give me some reference for this kind of dummy use?

You missed the point. The trick is to creat two masses (i.e. atoms without
charge and LJ parameters, so without any interactions), at the appropriate
distance (use a constraint) to reproduce moment of inertia. Then, use the
dummy atom constructions (see manual), to create three 'dummy' atoms at the
approprate relative positions, these 'dummies' are your 'real' C and O atoms,
and are the sites of the LJ and Coulomb interactions (and have no mass).

It would look a little like this:

	O--M-----C-----M--O


-- 
Groetjes,

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