I want to know what does constrain minimization means. Does it mean Keeping the backbone fixed and just minimizing the side chains? I also want to know that which would be a better option regarding the docking of ligand in the protein. Would it be better that i first perform the molecular dynamics of the protein and dock the ligand in the different confirmation that i obtain after simulation. Or would it be better to first dock the ligand and then perform the simulation (Molecular dynamics) and select the best pose my calculating the binding energy.