GROMACS version: 2020.1
GROMACS modification: No
I am comparing a number of protein unbinding PMF estimations done with Umbrella Sampling. My proteins are straight helices that associate through a hydrophobic interface. Up until now, I was using the pull code with the helices COM as reaction coordinate, which works great, but because the pull setup only takes into account the distance between the COMs, sometimes the helices rotate, or stick on one side of the other one. In order to make the different simulations more easily comparable, I would like to make the pulling procedure more standarized.
I would like to know if there is any way to ‘force’ the pulling simulation to keep both helices straight while they are being pulled apart. I have tried the cylinder pull coordinate, but it does not work quite as I wanted. I have also tried setting up two pull coordinates, one in each side of the helices, but this tends to break the helices in the middle.
Before I attempt to set up a custom collective variable with PLUMED, can anyone think of something within gromacs itself?
Kind regards and thank you for your time