[gmx-users] Cationic Dummy Atom Method

[Maik Goette]

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).

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
-- 
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/