I'd like to create an electrostatic energy profile as a function of distance between three positively charged residues that are stacked. I'm using the following commands:
skipe all excl elec
inte sele segid A .and. @resi1 end sele segid B .and. @res2 end
The two closest residues are about 5A apart and the inte results range from 3 to 21 kcal/mol. I expect variation because the distances of these residues range from 5 to 9 Angstroms during the simulation, but if the electrostatic interaction energy is so repulsive - why isn't my simulation exploding? Does inte take into account charge shielding by water molecules? I'm using a 12A cutoff.