GROMACS version: 2025.1-gcc
GROMACS modification: No
Hi,
I’m trying to apply flat-bottomed potential to my sistem that consists of a hydrophobic phase (slab of octanol molecules) in which a protein is partially inserted, and water in the rest of the box. The hydrophobic phase-water interface is at approx. x=9nm.
As I’m performing a pulling of the protein out of the hydrophobic phase into the water part, I would like to restrain the hydrophobic phase to it’s original space - i want a potential “wall” at x=9nm, only applied to the molecules of hydrophobic phase (octanol), so they can’t be dragged with the protein, yet they can move freely in the slab.
The most appropriate option for such a restraint is apparently a flat-bottomed potential, but there is almost zero explanation on how to apply it. I created a posres_FB.itp file which goes like:
[ position_restraints ]
; atoms functype g r k
1 2 4 9.0 1000
…
So the pulling still dragged a part of the octanol slab with the protein. I’m not sure if the g should be 3 or 4 to impose a potential at x=9, and also by looking at the FB potential graph ( Restraints - GROMACS 2025.1 documentation I’m not sure if r should be 9 or 4.5?
Or is it something else I’m doing wrong or missing?
Thanks