Maintain COM between two groups within a range (Equilibrium simulation)

GROMACS version: 2018

Hello All,

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.



You might want to consider pull-coord1-type=flat-bottom / flat-bottom-high. You would need two such coords, one with pull-coord1-type=flat-bottom and pull-coord2-type=flat-bottom-high