[gmx-users] MD simulations of flexible CO2

[iskarmou at cc.uoa.gr]

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)?
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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