From: Ramin Ekhteiari (
Date: Wed Jun 25 2014 - 11:45:33 CDT

Hi dears, I 'm trying to calculate the non-binding energies of hundreds of amino acid residues during MD simulation by using NAMD energy plugin. I preform this calculation one by one for each amino acid residue (e.g. resid 24 with resid 36), so it takes a lot times, Is there any  way for calculating these at one run and creating output of pair of residues interactions. Would be grateful for any advice. Cheers, Ramin