[gmx-users] rigid linear molecules
feenstra at chem.vu.nl
Thu Sep 18 09:08:01 CEST 2003
> 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:
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Room P275 Tel: +31 20 44 47608 Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "What If None Of Your Dreams Come True ?" (E. |
| | Costello) |
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