[gmx-users] g_dipoles, a bug?

[xieyh at hkusua.hku.hk]

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?


Thanks,
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