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I guess I am volunteering to add these (unless in some case other people feel like they know it better).
* We introduced alchemical metadynamics, allowing one to treat the alchemical variable as a …
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I would like to perform fully charge self-consistent DFT+DMFT calculations with spin-orbit coupling (SOC) using TRIQS. Does the current version of DFTTools in TRIQS support this feature? If not, I am …
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We are currently working on obtaining free energy information for a large protein complex using a coarse-grained Martini model in OpenMM. However, we've encountered challenges in aligning our calculat…
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I'm running through the code and am a bit confused on some of the code choices. For example, For example, B1 and B2 solvent files have different lambda restraints.
bond_energy_function = "lambda_re…
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We should eventually include vibrational calculations so that we can compute free energies, etc.
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**In broad terms, what are you trying to do?**
The [Diamond Light Source XChem facility provides a fragment screening service](https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html) for …
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Simulations can crash (give NaN errors) if the protein has not been equilibrated first. Maybe we could add a warning or note in the documentation that proteins may need to be equilibrated (short minim…
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**In broad terms, what are you trying to do?**
The [COVID Moonshot](https://postera.ai/covid) and its successor, [ASAP](https://www.choderalab.org/news/2021/10/26/asap-avidd-proposal), are pursuing…
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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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I want to try to simplify the way standard state corrections are incorporated in Yank, and was hoping to get suggestions from @luirink and @davidlmobley.
For generality, Yank uses the concept of "pha…