Murat,
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
(etc)
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).
David
On 6/19/06, MURAT CETINKAYA <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]>
I think I've seen this one in the archives before. Did you try
searching the list?
On 6/19/06, MURAT CETINKAYA <[EMAIL PROTECTED]> 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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