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Dec 14, 2019 at 15:36 comment added Matteo Ferla Totally correct for MD. However, a wee note: most ligand docking program use implicit water (except special case such as WaterDock), which means that TIP3P waters or similar are not added, but a fudge factor is used to account for the dynamic but stabilising polar properties of water.
Nov 14, 2019 at 14:46 history answered fra CC BY-SA 4.0