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Dear openmmtools team,
I am trying to calculate the hydration free energy of pyrene molecule in a water/DMSO mixture and obtain nonphysical results.
Here is a brief description of what was done:…
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For electron-positron pair production by photons: When sampling the energy asymmetry `x = E_electron / (E_electron + E_positron)`, one would expect a symmetric distribution.
If I sample a distribut…
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We start with #474 to use a different theme. This allows very easy way to write docs in markdown (is also currently supported but doesn't format as nicely).
Todos:
- [ ] Move the dataset module …
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Especially if this ends up being a per-release benchmark run, it would be good to have a simple manner for folks to work out what historical computed free energies were for a given edge based on a giv…
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Hello,
Thank you for making and maintaining this tool.
I'm trying to figure out the best folding for a sequence of unknown length, so I'm trying all reasonable sequence lengths 2-100 nt
the issue…
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For the latest development code I get:
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* MPI error 672736783 in mpi_cart_sub @ mp_cart_sub : Other MPI …
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It would be useful if we could refactor [`stats.py`](https://github.com/OpenFreeEnergy/cinnabar/blob/main/cinnabar/stats.py) into a class API so that we could drop in different solvers.
Right now, …
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I would like to calculate the dG of a ligand binding to a protein via the LIE method:
dG = alpha(Uvdw(bound) - Uvdw(free)) + beta(Uelec(bound) - Uelec(free)) + gamma
It appears that some special s…
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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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It would be useful to have a lightweight package for easily reading, interrogating, manipulating, and doing analysis of the JSON analysis files we generate from fah-xchem. To do this, we currently nee…