A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine for instance on a docking based alignment to prepare the input of a FEP calculation.
This is a companion discussion topic for the original entry at https://kni.me/w/XWgCAIYZi4EgfcJP