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dwhswenson merged 1 commit into from
May 13, 2023
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update tutorial to mention complex of vacuum #65

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2 changes: 1 addition & 1 deletion rbfe_tutorial/python_tutorial.ipynb
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Expand Up @@ -189,7 +189,7 @@
"\n",
"The `LigandNetwork` only knows about the small molecules and the alchemical connections between them. It doesn't know anything about environment (e.g., solvent) or about the `Protocol` that will be used during the simulation.\n",
"\n",
"That information in included in a `Transformation`. Each of these transformations corresponds to a single leg of the simulation campaign, so for each edge in the `LigandNetwork`, we will create two `Transformation`s: one for vacuum and one for solvent.\n",
"That information in included in a `Transformation`. Each of these transformations corresponds to a single leg of the simulation campaign, so for each edge in the `LigandNetwork`, we will create two `Transformation`s: one for the complex and one for solvent.\n",
"\n",
"In practice, this will be done for each edge of the `LigandNetwork` in a loop, but for illustrative purposes we'll dive into the details of creating a single transformation. In particular, we'll create the solvent leg for the pair of molecules we selecting for the mapping above."
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