[gmx-users] Three-site model for acetonitrile

Anton Feenstra feenstra at chem.vu.nl
Tue Feb 25 18:24:28 CET 2003

Christoph Freudenberger wrote:
> Hi David,
> David wrote:
>> This is why I was aking about how you keep it linear. The angle will not
>> work, or will be rather instable at best, since the potential is not
>> continuous at 180 (i.e. angle <= 180 always). You probably want to
>> define the C as a dummy particle. Note that you will have to
>> redistribute the mass over N and CH3 such that centre of mass is
>> unchanged and inertia tensor is not modified too much either.
> I just read anything about constraints and dummies in the manual and i
> think i'm beginning to understand the concept.
> Does this topolgy make sense?

It seems quite OK, however it seems you simply moved mass from the
C to the Me and N atoms (I'm not sure, since I don't know the exact
masses of the atoms). This will influence the moments of intertia
of your molecule (i.e. it will tumble slower).

The way to do this more accurately, is to calculate the inertia tensor
for your normal, three mass molecule, and then calculate the distance
and masses for a two mass system with the same total mass and the same
inertia tensors. For a linear molecule, this is quite trivial to do.
You will find that the two masses will need to be closer together than
your Me and N atoms are. Then, if you have the two masses at their
appropriate distance, you construct *all* *three* atoms (Me, C and N)
from the two dummy masses.

You will now have a system of two masses that accurately reproduce
the mass and moments of inertia of acetonitile and three 'dummy' atoms
that accurately reproduce the normal atomic interactions of acetonitrile.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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