When pulling a group of a simulation system, how does each atom feel the pulling force?

User discussions
1

GROMACS version:
GROMACS modification: No

Suppose two groups A and B (e.g, a protein and a ligand).
We want to pull one group to dissociate.
Then steered MD (SMD) would be a good choice. SMD pulls the centre of mass of one group to dissociate it from the other group.

Then I have a question:
(1) Does each atom feel the pulling forces?
(2) Do the pulling forces act only on the COM of one group?
(3) Do the pulling forces act on each COM of the two groups with the force direction being opposite?

Thanks,

2

Hi,
here you find more on pull code in GROMACS and maybe the answers to your questions Non-equilibrium pulling — GROMACS 2021.3 documentation
\Alessandra

3

Thank you for your reply. I have looked into the document. I think that Eqn (6) in the URL is the one that expresses how a pulling force acting on the centre of mass of a pull group is distributed into each atom. Am I correct?