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I'm looking at the RMSE (in kcal/mol?) vs iteration plot from the `300_adaptive_3gbmodel_largejoint_days.h5` dataset.
Any idea why the initial RMSE would be ~13 kcal/mol? What parameter set was the …
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1) specify available units and type of notation (i.e. kcal/mol vs kcal.mol-1 and kJ/mol or eV or..)
2) Everything seems crystal clear except the meaning of "(When the --relative flag is specified i…
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[Siebenmorgen, Till, and Martin Zacharias. “Computational Prediction of Protein–Protein Binding Affinities.” *Wiley Interdisciplinary Reviews: Computational Molecular Science* 10, no. 3 (2020).](https…
cramg updated
3 years ago
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Hello,
I find it hard to get information on how to use kwargs to compute the effects of **partial pressures on Gibbs free energies**.
I've managed to do some calculations by trial and error aft…
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Using this issue to track and plan the next features. Any additional, comment in this issue and this top post will be edited to include them, link to sub-issues, and list relevant PRs for each item.
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Here is the run I am trying to replicate. Below, are the inputs: the two sample sequences, and using DNA parameters.
![image](https://github.com/ViennaRNA/ViennaRNA/assets/124276755/d49417a6-734c-4…
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[Kumari, Rashmi, Rajendra Kumar, Open Source Drug Discovery Consortium, and Andrew Lynn. “G_mmpbsa —A GROMACS Tool for High-Throughput MM-PBSA Calculations.” *Journal of Chemical Information and Model…
cramg updated
3 years ago
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cramg updated
3 years ago
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I'm tracking down an odd issue where it seems like the `pint.Quantity` wrapped `np.float32` is causing problems when `molecule.to_openeye()` is called afterwards:
```
Traceback (most recent call las…
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Hi all 😄
So, I'm currently trying to create a dataset from an observation. I have full enclosure IRFs with a Background3DModel which is constructed from ON data using the exclusion background meth…