[gmx-users] Cationic Dummy Atom Method

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 17 08:47:04 CET 2005

On Thu, 2005-02-17 at 11:30 +0100, Maik Goette wrote:
> Dear GMX-Users,
> I am trying to simulate a complexed zinc ion with the cationic dummy 
> atom method (Pang,1999) in Amber FF.
> In this Method the Zinc-Ion is mimicked by a central uncharged Zinc 
> (full mass) atom and 4 tetrahedric dummys with 0.5 charge each and very 
> small mass (0.1).
What kind of distance are these positive particles at? In vacuum you
want to limit rotation about the center of mass otherwise it starts
spinning. Try it in water instead.

You could try to define the four charges as atoms connected by
constraints, and the central Zn as a dummy.

> I even tried to simulate one such Zn-Model in Vaccum (G43b1), but it 
> really "explodes". The EM deliveres fine results...But the MD just 
> finishes it off.
> I tried anything from no mass to large mass for the dummies, no charge 
> at all, 2- charge on the center atom...nothing. Lincs and shake were 
> tried. In vacuum, shake seems to work (except for delivering a 
> "error"-pdb each step, so it may not work...end-structure is fine), but 
> in water it's failing again.
> Has anyone tried out this method with GROMACS?
> Maybe it just doesn't work with GROMACS...
> Any hint is welcome
> Regards
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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