[gmx-users] g_dipoles, a bug?
spoel at xray.bmc.uu.se
Fri Apr 15 17:14:55 CEST 2005
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 ]
> 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 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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