[gmx-users] g_dipoles, a bug?

[David]

On Sat, 2005-04-16 at 17:47 +0800, xieyh at hkusua.hku.hk wrote:
> Dear Dr. David:
> 
> If my dummy atoms are cooperated into protein as one molecule, is it possible to
> separately calculate the dipole of dummy?
Not unless you make a topology that defines one molecule as only the
dummy. But if they have charge 0 they have dipole 0. 
> 
> 
> Xie Yinghong
> Hong Kong Univ.
> 
> > Dear Dr. David:
> > 
> > I think I have almost understood your meaning about molecule number.
> > Now can you give me a confirmation, for example, in the last part of 
> > my .top file:
> > ...
> > ...
> > [ molecules ]
> > protein    1
> > DNA        1
> > dummy      1
> > SOl     1000
> > 
> > Then that means the dummy should be the 3rd molecule in my system. So, if I
> want
> > to get the dipole of dummy atoms. I need to define my index.ndx file as:
> > 
> > [ dummy ]
> > 3
> > 
> > Is it correct?
> 
> >Yes.
> 
> 
> 
> 
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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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