[gmx-users] rigid linear molecules

Lanyuan Lu lulanyuan at sina.com
Thu Sep 18 14:59:01 CEST 2003

I see the point now. But I'm still wondering that whether this method is widerly used by others in literature. I mean, can I use this directly to write a paper ( which reference should I cite? ) or need I do a lot of test first to justfy the model?
Thanks for all kind help.
Lanyuan Lu
----- Original Message ----- 
From: "Christoph Freudenberger" <christoph.freudenberger at chemie.uni-ulm.de>
To: <gmx-users at gromacs.org>
Sent: Thursday, September 18, 2003 7:39 AM
Subject: Re: [gmx-users] rigid linear molecules

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