[gmx-users] g_dipoles, a bug?

[xieyh at hkusua.hku.hk]

Dear Dr. David:

If my dummy atoms are cooperated into protein as one molecule, is it possible to
separately calculate the dipole of dummy?


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.