[gmx-users] Cationic Dummy Atom Method

[David van der Spoel]

On Fri, 2005-02-18 at 09:54 +0100, Maik Goette wrote:
> Thanks for the answer
> 
> Distance Zn-DUM: 0.9A
> Dist DUM-DUM: 1.47A
> 
> Oh, spinning would be ok. Main thing is, that it sticks together.
> In water, similar problems occur. Thats why I tried vacuum.
> 
> The four charges are defined as dummy atoms (mass 0.1, no VdW, charge 
> 0.5) and are connected to each other and the central atom via bonds.
> Angles and dihedrals are defined also. That is probably the reason, why 
> EM produces a superb tetrahedral conformation.
> I dont't see the advantage of the dummy in the center, but I'll try it.
> 
Check whether the bonds to the dummies are there in the tpr file. I
think grompp removes them unless you use the -normvsbds flag (or similar
in older gromacs)


> 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/
> 
> 
> David van der Spoel wrote:
> > 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
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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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