[gmx-users] g_dipoles, a bug?

[David van der Spoel]

On Fri, 2005-04-15 at 20:41 +0800, xieyh at hkusua.hku.hk wrote:
> 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...
> 
> Another question, if part of atoms are frozen in my system, which ensemble (NVT
> or NPT) should be better?
I think the pressure may be wrong if you freeze stuff, in which case NVT
should be better. I'm not sure though.

> 
> Thanks a lot.
> 
> 
> Xie Yinghong
> Hong Kong Univ.
> 
> 
> 
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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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