From: Ramin Ekhteiari (
Date: Mon Jul 07 2014 - 14:59:42 CDT


I'm trying to calculate pair interaction energy between protein and ligand via NAMD energy plugin. In the active site of the protein near the ligand, there are only 2 or three water molecules were placed, so how should I set the dielectric constant, should it be 1 or more ?

I will appreciate for your answers.