In systems of such kind, everything will depend on the atom of the ligand, which coordinated by copper ion.
Perform ab initio geometry optimization and find the optimal distance. Then adjust sigma(s). Dr. Vitaly Chaban There is a copper ion with four ligands in my system. I am going to > study this system using MD simulations. > For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from > one paper will be used in our > simulations. I already found the parameters of copper ion (Cu2+) in the > OPLS-AA/L force field files: > sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without > ligands. The two epsilon are the same, > just with different units. > > My question is that I do not know how to convert the vdW radius to > sigma. I found that the vdw radius of copper is > 1.4 angstrom, and the sigma in the force field file is 2.08470e-01. > Could someone tell me how to do the converting? > > Thanks very much! > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
