[gmx-users] rigid linear molecules

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Thu Sep 18 13:41:01 CEST 2003

Anton Feenstra wrote:
> 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

Hi lulanyuan,

It was me, who started the disscusion about rigid models for linear
molecules some time ago and I managed to create a topology for
acetonitrile with the help of David, Anton and some others.
You can download this topology from the molecules site and use
it as a template for CO2.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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