[gmx-users] Cationic Dummy Atom Method
mgoette at mpi-bpc.mpg.de
Fri Feb 18 09:54:09 CET 2005
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.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
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/
David van der Spoel wrote:
> On Thu, 2005-02-17 at 11:30 +0100, Maik Goette wrote:
>>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
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