[gmx-users] Three-site model for acetonitrile

[Anton Feenstra]

christoph.freudenberger at chemie.uni-ulm.de wrote:
> 
> Zitat von David <spoel at xray.bmc.uu.se>:
> 
> > On Wed, 2003-02-26 at 17:46, Christoph Freudenberger wrote:
> > > [ dummies2 ]
> > > ;  ai    aj    ak       funct   a
> > >      3     1     2       1       0.2652197
> > >      4     1     2       1       0.8203527
> > >      5     1     2       1       1.2652197
> > Shouldn't one of these numbers be negative, or is the dummy further out
> > than the atom?
> no, that's fine D1 is ~0.2nm away from the com, D2 is ~0.06nm.

Your (Christoph's) equations look fine, but the numbers in your
topology don't make sense to me.

First, your constraint distance between the masses is 0.263, while
your Me-N distance (from a previous topology in your mail) was 0.262.
In other words, your masses are *further* out than your atoms, which
cannot be true, since if you shift mass (from the C) outwards, your
moments of inertia increase which must be balanced by shifting the
two masses inwards with respect to the positions of the atoms.

Also, since Me (15.035) and N (14.0067) are about the same mass, I'd 
expect the mass distribution over D1 and D2 to be much more symmetric.

It should go a little something like this (Tag Team):

	Me-D1---C---D2-N

with coefficients in the order of -0.1 for Me, 0.5 for C and 1.1 for N,
when constructing from D1 D2 (in that order), as Me is left of D1 (<0),
C is roughly in the middle and N is right of D2 (>1).



-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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