[gmx-users] g_dipoles, a bug?
spoel at xray.bmc.uu.se
Sat Apr 16 10:38:41 CEST 2005
On Sat, 2005-04-16 at 16:29 +0800, xieyh at hkusua.hku.hk wrote:
> 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 ]
> Is it correct?
> Xie Yinghong
> Hong Kong Univ.
> > On Fri, 2005-04-15 at 23:01 +0800, xieyh at hkusua.hku.hk wrote:
> > > Dear David:
> > >
> > > I can not under that g_dipoles interpret the atoms numbers as
> > molecule numbers.
> > > For example, I have a system as the follows:
> > > atom 1 ~100: my molecule
> > > atom 101~120: dummy atoms
> > > atom 121~500: water
> > > When I use g_dipoles, I choose the group "101~120". Anything is
> > wrong? Because
> > > my result for dipole moment of dummy atoms is actually not equal to
> > zero.
> > >
> > g_dipoles interprets this as molecule 100 to molecule 120. Check your
> > tpr file (using gmxcheck) for the molecule numbers (or your .top
> > file).
> > If your dummy atoms together are e.g. molecule 6 then your index file
> > should only contain:
> > [ dummies ]
> > 6
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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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