[gmx-users] oplsaa force field and dummy atoms

[MURAT CETINKAYA]

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