[gmx-users] g_dipoles, a bug?

[David]

On Fri, 2005-04-15 at 22:11 +0800, xieyh at hkusua.hku.hk wrote:
> Dear Dr. David:
> 
> I am very sure that I used an index file to refer to the dummy atoms. 
> 
> g_dipoles -f full -s full -n index -o Mtot
> 
> and then chose the group only including dummy atom numbers.
Yes, but g_dipoles interprets the atom numbers as molecule numbers. In
other words you can only analyse complete molecules. And if they have no
charge they won't have a dipole either.
> ...
> 
> 
> Xie Yinghong
> Hong Kong Univ.
> 
> 
> 
> >> Dear users:
> >> 
> >> Who ever successfully applied "g_dipoles" program? I met a very strange
> >problem
> >> in my analysis.
> >> 
> >> I defined some dummy atoms (without mass and charge) in my simulated system,
> in
> >> principle, the total dipole for such dummy group should be zero owing to its
> >> non-charge. However, when I used the g_dipoles to analyze, I found that the
> >> dipole for dummy is far away from zero, I do not what is the reason. Any
> >> suggestion?
> 
> >Are you using an index file? g_dipoles assumes numbers in index files
> >are molecule numbers rather than atom numbers...
> 
> 
> 
> 
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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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