GROMACS version: 2018
I want to run a simulation where I want the center of mass distance between two groups to be maintained within a certain distance (example 0.5 to 1 nm) in an equilibrium simulation.
I think I can use the pull code with pull-rate = 0, but then how do a let the distance to vary between 0.5 to 1 nm between the two groups? Just use a weaker force-constant?
I am not sure how to use gmx genrestr to set this up between two different groups.
I will greatly appreciate the suggestions, thanks in advance.