[gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

[Sajeewa Pemasinghe]

Hi all,

I have a system in which I need to maintain the center of mass distance
between two molecules constant for an umbrella window. The structures are
not strictly aligned along an axis as they are the product of an
equilibrium simulation.I have the following code.

pull = umbrella
pull_ngroups = 2
pull_group1_name = molecule1
pull_group2_name = molecule2
pull_coord1_type = umbrella
pull-geometry = distance
pull_coord1_groups = 1 2
pull-dim = Y N N
pull_coord1_rate = 0.0
pull_coord1_k = 2000

I have the following questions.

1) Does pull-dim = Y N N mean that the k=2000 is applied along the x
coordinates only in maintaining the distance constant?

2) If I want to apply a harmonic potential to maintain the distance along
both x and y axis constant (in maintaining the distance *r* constant) do I
have to make the following changes?

pull_coord2_groups = 1 2
pull-dim = Y Y N
pull_coord2_k = 2000  # this is applied on the y coordinate (that is the
picture I have in my mind)

I am really confused here. I really appreciate some help with this.

Thank you very much

Sajeewa