[gmx-users] Cationic Dummy Atom Method

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Feb 17 11:30:53 CET 2005

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

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

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