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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
