While following the proteins and protein-DNA complex tutorial, I discovered that the non-bonded interaction parameters vary for the same types of beads. Upon comparing the Q0-Q0 non-bonded interactions in two .itp files (
www.cgmartini.nl/images/parameters/ITP/martini_v2.1.itp
and
www.cgmartini.nl/index.php/force-field-parameters/dna
), I noticed that they yield different values. I am curious to know the reasons behind these discrepancies.