[gmx-users] Umbrella sampling with restraint on the center of mass of ligand

[gmx user1]

Dear GMX users

I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00624 ;
https://www.sciencedirect.com/science/article/pii/S0005273615004319?via%3Dihub
)

Yet, I am not certain of which .mdp settings I should use to accomplish my
goal, the documentation is not clear and most infomation I find
refers to the application of harmonic potentials when the reaction
coordinate is a distance between two groups.

Here are my .mdp settings:

pull                    = yes
pull_print_com          = yes
pull_print_ref_value    = yes
pull_nstxout            = 500
pull_nstfout            = 0
pull_ncoords            = 1         ; only one reaction coordinate
pull_ngroups            = 1
pull_coord1_geometry    = direction-periodic
pull_coord1_vec         = 0 0 1
pull-coord1-origin      = 0 0 0
pull_group1_name        = LIG
pull_coord1_groups      = 0 1
pull_coord1_type        = umbrella  ; harmonic potential
pull_coord1_start       = yes       ; define initial COM distance > 0
pull_coord1_rate        = 0.0       ; restrain in place
pull_coord1_k           = 500      ; kJ mol^-1 nm^-2

Essentially, I created a vector between the center-of-mass of the ligand
and an absolute reference (0,0,0) and I had to use pull_coord1_geometry =
direction-periodic ( instead of direction) ,because the simulation crashed.
This also forces me to perform an NVE simulation.

Is this the right way of applying a an harmonic restraint on the
center-of-mass of a ligand for umbrella sampling? Are these settings
correct?

Any help is appreaciated.

Thanks in advance