[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

Sonia Aguilera sm.aguilera37 at uniandes.edu.co
Mon Sep 17 21:38:32 CEST 2012

Hi Justin, 

So, are you saying that I should use my topoly file with all the original
charges for both none-vdw and vdw-vdw-q calculations? I understand that the
couple-lambda* setting dictate which parameters are involved in both
calculations. However, in your tutorial you set all charges to zero with the
same settings in the mdp file. Can you please make this clear for me? Should
I use the topoly file with the original charges for both calculations?

Thank you, 

Sonia Aguilera
Graduate Student-Chemical Engineering Department
Universidad de los Andes

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