[AMBER] The effect of water box size for TI free energy calculation

From: zz sheng <shengzizhang.gmail.com>
Date: Thu, 27 Jan 2022 00:17:57 -0500

Dear All,

For using thermodynamics integration to predict relative free energy change (ddG), I wonder if the sizes of the water box for the protein-ligand and ligand alone MD have to be the same, like 10Å from the solute. Will the water box size affect ddG calculation (i.g. 5Å for the complex and 10Å for the ligand)?


Thanks,

Best,

Zizhang Sheng


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Received on Wed Jan 26 2022 - 21:30:02 PST