[gmx-users] oplsaa force field and dummy atoms

[MURAT CETINKAYA]

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