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MobleyLab / benchmarkff

Compare optimized geometries and energies from various force fields with respect to a QM reference.
MIT License
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Explore possibility of shallow potential energy surfaces for high TFD (low ddE) molecules #8

Open vtlim opened 4 years ago

vtlim commented 4 years ago

From Alberto Gobbi:

One way to test the shallow surface hypothesis would be to compare the energy trace during the geometry optimization. Or you could use constraint minimizations. We are computing strain energy using a combination of conformational sampling and constraint minimization that allow to see how shallow the surface is around the starting point:

Lee, Man-Ling, Ignacio Aliagas, Jianwen A. Feng, Thomas Gabriel, T. J. O’Donnell, Benjamin D. Sellers, Bernd Wiswedel, and Alberto Gobbi. “Chemalot and Chemalot_knime: Command Line Programs as Workflow Tools for Drug Discovery.” Journal of Cheminformatics 9 (June 12, 2017): 38. https://doi.org/10.1186/s13321-017-0228-9.

I think the original work is by Bostroem: Boström J, Norrby PO, Liljefors T (1998) Conformational energy penalties of protein-bound ligands. J Comput Aided Mol Des 12(4):383–396