[gmx-users] Doubt about Steered molecular dynamics

[Quyen Vu Van]

Hi Everyone,
Please help me to understand about COM Pulling in gromacs?
As I understand from Justin's tutorial, a dummy atom will be attached to
the center of mass of Protein A through a spring with a force constant of
1000kJ / mol / nm ^ 2 (pull_coord1_k) and pulling along the positive
direction of the z-axis, dummy atom will move at a constant velocity
(pull_coord1_rate)
The pullf.xvg file contains the force that the spring acts on the center of
mass of Protein A, right?

In the manual of gromacs says:
*pull_coord1_type = umbrella*


*A harmonic potential is applied between the centers of mass of two groups.
Thus, theforce is proportional to the displacement  *
What is the force in the manual means? Are two groups here Protein A and
Protein B or somewhat?
Is there any pulling force acts on Protein B?

Thanks,
Quyen