Protein association, helix group, PMF

Dear all

I want to do a two protein association simulation, both protein contains four helix.
Can I use make_ndx to group the each helix and calculate the PMF between the two protein’s helices separately?

The definition of the most appropriate reaction coordinate can not be generalized since it is system and problem specific. It can occur that one has to try different reaction coordinates.
But yes, you can create the two independent groups using gmx make_ndx and the use the pull code to calculate the pmf along a reaction coordinated (for example) defined by the com distance between the two groups.
Best regards