[gmx-users] g_dipoles, a bug?
spoel at xray.bmc.uu.se
Sat Apr 16 12:09:45 CEST 2005
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
> > to get the dipole of dummy atoms. I need to define my index.ndx file as:
> > [ dummy ]
> > 3
> > Is it correct?
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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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