[gmx-users] g_dipoles, a bug?

[David]

On Fri, 2005-04-15 at 12:47 -0400, VISWANADHA SRIDHARA wrote:
> Just continuing this discussion, does g_dielectric takes numbers in
> the index file as atom numbers, unlike g_dipoles, which takes them as
> molecule numbers?
> 
It doesn't read an index file, just the Mtot.xvg file that comes from
g_dipoles.

>  
> 
> David <spoel at xray.bmc.uu.se>
> Sent by: gmx-users-bounces at gromacs.org
> 04/15/2005 05:14 PM ZE2Please respond toDiscussion list for GROMACS
> users 
> 
> To   Discussion list for GROMACS users <gmx-users at gromacs.org>
> cc   
> bcc   
> Subject   Re: [gmx-users] g_dipoles, a bug?
>  
> 
> 
> 
> 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
> 
> 
> >
> > Thanks,
> >
> > Xie Yinghong
> > Hong Kong Univ.
> >
> >
> >
> > >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.
> >
> >
> >
> >
> > _______________________________________________
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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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-- 
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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