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When propagating the error for the fitted spectrum, there is an error if the source position is free in the fit (see PR [#78](https://github.com/cositools/cosipy/pull/78)).
We define `results_err =…
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When calculating the binding free energy change caused by mutation of protein amino acids using AMBER's TI for FEP, when calculating the complex, the energy calculated in a certain window is negative …
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**Summary**
The free energy calculated by VASP and stored in a pyiron HDF5 file is not consistent when the D3 (VDW) correction is enabled.
**pyiron Version and Platform**
- Python Version: 3.…
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I'm finally in the process of changing from using single-point energies to one-sided EXP estimates of free energy differences for implicit solvent hydration free energies.
@kyleabeauchamp: You can mo…
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### General
- [X] My feature does not exist in the latest version of MySpeed.
- [X] I have checked that my feature has not been suggested by anyone else.
### Your Idea
I would love the ability to a…
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Hi, thanks for the great project!
I was a bit surprised to see that the examples here (and in the yank-examples repo) for hydration free energy include not one thermodynamic leg (decoupling the sol…
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**Description**
A handful of NaNs were produced using the following mesh with large numbers of computational ions when ions initially at the top of the mesh hit the bottom of the first trench:
```…
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### Contact Details
sd20163818@snu.ac.kr
### What happened?
Hi.
I'm trying to run RNAfold on presumably 'circular' RNA sequences. I ran it on about 400000 sequences (fasta file), but the RNAfold r…
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Hello,
the TWCManager show me the correct free energy from the Solar System, but load with max 11KW and not with the free 5KW.
attached a screenshot.
![image](https://user-images.githubusercont…
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The Green web foundation API and datasets have historically had a really binary green/grey definition, which is easy to use, but hides a colossal amount of detail.
Tor example there's a whole issue…