Dear all,
I am trying to compute interaction energy between two peptides in my
system. If I am using PBC=no in my mdp file for rerun, the coulomb
interaction energy becomes positive but this part was negative while
using the PBC = XYZ with the same cutoff in both cases. This is
unexpected and I am not able to interpret the result.
Can you please help me to fix it?
Changing periodic boundary conditions between the simulation and recomputing energies is meaningless.
Note that computing interaction energy is not useful in most cases. What is relevant is the free-energy, not interaction energies as they do not account for entropic effects. Also I assume your peptides are solvated and most interactions are mediated by the solvent.