[gmx-users] Umbrella Sampling

[Steven Neumann]

Dear Gmx Users,

I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.

I pulled my molecule away and two ions were also detached from the protein
surface being attached to my ligand.

My question: if I run my US caluclation and combine windows by WHAM (I
specified in my umbrella.mdp my ligand as a pull_group1 and same protein
residues I pulled it from as pull_group0) will get the PMF profile for my
ligand binding or ligand and two ions binding?

Steven