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. Author manuscript; available in PMC: 2023 Mar 8.
Published in final edited form as: J Chem Theory Comput. 2022 Feb 11;18(3):1359–1381. doi: 10.1021/acs.jctc.1c00590

Figure 5:

Figure 5:

It is challenging to rehydrate the target site (red) in (A) The thrombin system (PDB: 2ZFF). Bar graphs show the water occupancy of the target site in (B) unbiased MD simulations with ordered water molecules removed prior to simulations, (C) unbiased MD simulations with ordered water molecules retained prior to simulations, (D) grand simulations and (E) grand simulations with position restraints on heavy atoms of the protein and all atoms of the ligand. All ordered water molecules were removed prior to grand simulations in (D-E).