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### Describe the bug
I am trying to fit a custom spectrum which has spectral data below 1 keV (though not usable). I am trying to fit the spectra with above 1 keV using `spec.energy_fitting_range` at…
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[Sun, Huiyong, Youyong Li, Sheng Tian, Lei Xu, and Tingjun Hou. “Assessing the Performance of MM/PBSA and MM/GBSA Methods. 4. Accuracies of MM/PBSA and MM/GBSA Methodologies Evaluated by Various Simul…
cramg updated
3 years ago
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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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There are a few things we should make sure we're doing in perses to get good, robust protocol work measurements:
* Use the `DeterministicForces` platform property so that PME gives deterministic ener…
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Great paper! Here are a few items for your consideration...
page 20, 5 lines above section 7: practise-->practice
page 22, second bullet: cyro-->cryo
page 22, first bullet in Affinity data ("…
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Right now, we subtract the mean calculated ΔG and mean experimental ΔG and plot, making for a ridiculous plot that include ΔG >= 0 (Kd > 1 Molar), which is totally nonsensical for an absolute ΔG.
!…
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This is related to #3166 where I am trying to write a class that creates an alchemical hybrid system for running relative free energy calculations. The hybrid system will handle:
1) alchemical modif…
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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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Yesterday I defended my master's thesis, and my supervisor has approved my thesis as complete. The XPS spectrum was analyzed with LG4X and plotted with Matplotlib after I exported the data.
The sad…
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I'd like to refactor and reorganize the package structure to be more sensible.
This doesn't need to be done immediately, but the sooner the better.
Here's what I propose:
* `perses.analysis` can …