[gmx-users] MD simulations of flexible CO2

[David van der Spoel]

On Wed, 2005-05-25 at 10:45 +0300, iskarmou at cc.uoa.gr wrote:
> Dear Prof. Van der Spoel.
> First of of all thanks for your answer.
> But could you explain in more details, the features
> (geometries, constraints,intramolecular interactions, etc) of this
> 4-site potential model that you mention (using a dummy paricle)?
It's described really well in the manual, chapter 5. You define two
oxygens with a bond between them and the carbon is just a linear
combination of the coordinates of the two oxygens.

> Regards
> I. Skarmoutsos
> 
> 
> 
> Αρχικό μήνυμα από  David <spoel at xray.bmc.uu.se>:
> 
> > On Tue, 2005-05-24 at 18:33 +0300, iskarmou at cc.uoa.gr wrote:
> > > 
> > > My question is the following:
> > > Concerning the MD simulation of fluid CO2, my problem is
> > > to obtain information about the reliability of the Gromacs
> > > software to use angle-bending potentials (in describing the
> > > intramolecular interactions) in the case of LINEAR! molecules.
> > You can't. You have to use a virtual site (dummy particle) on the axis
> > between the two oxygen. 
> > > Regards
> > > I. Skarmoutsos
> > >  
> > > 
> > > 
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> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
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> 
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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