Dear all, I have simulated myoglobin in water system. Now, I want to calculate the self interaction energy (Coulomb) of the protein. In that case shall I consider the interaction between the OE1 and OE2 atoms in glutamte, or other such pairs?
Including all pairs, except the bonded pairs, the average self-energy of the protein is coming as 8108 kT from my program. Is this value plausible? Any comment/suggestion is appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
