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**In broad terms, what are you trying to do?**
Calculate binding free energies using expanded ensemble simulations, AWH, or potentially simple "array of lambda" simulations. Hamiltonian replic…
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The hydration example refers to binding free energies of toluene in T4 lysozyme.
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You should take the fraction_contacts_expectation function in secondary_structure.py as the example. Instead of passing in a native contact list and a distance cutoff, you pass in a general function …
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We should eventually include vibrational calculations so that we can compute free energies, etc.
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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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I've been using YANK (0.23.4) to simulate a protein-ligand system (6069 atoms and water box and around 100 replicas for both the complex and solvent phase), on a system with two GTX 1080Ti GPUs, and s…
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@jchodera will draft a proposal on this issue for representing free energies and uncertainties (of various flavors) that generalize well across different alchemical protocols. We'll use that proposal …
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[Ruiter, Anita de, and Chris Oostenbrink. “Advances in the Calculation of Binding Free Energies.” *Current Opinion in Structural Biology* 61 (2020): 207–12.](https://doi.org/10.1016/j.sbi.2020.01.016)
cramg updated
3 years ago
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[Hayes, Joseph M., and Georgios Archontis. "MM-GB (PB) SA calculations of protein-ligand binding free energies." Molecular Dynamics-Studies of Synthetic and Biological Macromolecules (2012): 171-190](…
cramg updated
3 years ago
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We need to decide on the rest of the figures for the paper.
For example, we will need to summarize results of constant-pH simulations of complexes and their impact on free energies.