[gmx-users] oplsaa force field and dummy atoms

David Mobley dmobley at gmail.com
Tue Jun 20 20:23:26 CEST 2006


A dummy atom is a dummy atom. You can define it in your toplogy file,
so you don't have to use the preexisting ones defined by the force
field you're using. Just add appropriate entries in the atomtypes
section. For example, in one of my topologies, I have something like:

[ atomtypes ]
; name   bond_type   mass   charge   ptype     sigma   epsilon
c3          c3              0.000   0.000     A          3.39967e-01  4.5773e-01
dc3         c3             0.000   0.000     A          0.0000          0.0000

The first one is a normal atom (but I specify the mass and charge in
the [ atoms ] section); the second is a dummy atom (no LJ parameters).


On 6/19/06, MURAT CETINKAYA <cetinkayam at psu.edu> wrote:
> Yes, I did a detailed search about it. The confusing part is nobody complained
> about using dummy atoms. Am I missing something?
> thanks.
> From: "David Mobley" <dmobley at gmail.com>
> I think I've seen this one in the archives before. Did you try
> searching the list?
> On 6/19/06, MURAT CETINKAYA <cetinkayam at psu.edu> wrote:
> > Hi GMX users,
> >
> > My question is to calculate solvation free energy of a non-standard residue (I
> > managed to define it into oplsaa database). I followed the tutorial prepared
> by
> > groningen group
> (http://md.chem.rug.nl/education/Free-Energy_Course/index.html)
> >
> > My problem is how to use dummy atoms in ffoplsaa for my calculations. I think
> > DUM is for tip4p water and there are other types like MNH3 and MCH3A.
> Question:
> >
> > Can I use the already defined dummy atoms (MNH3 etc) for my system? I dont
> think
> > that these will be enough for my special molecule. Or, should I define new
> > dummy atoms having same bonded interaction parameters (which should have the
> > same procedure like defining the molecule originally). I hope my question is
> > clear enough :)
> >
> > Thanks in advance
> Murat CETINKAYA, M.Sc.
> BioNanoMaterials Group,
> Dept. of Engr. Science and Mechanics,
> The Pennsylvania State University,
> University Park, PA 16802
> office: (814) 863 9967
> web: www.personal.psu.edu/muc176
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