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i have done ligand simulation in water and now wantto calculate solvation free energy , i used 31 lambdas states, i got this error by using alchemical_analysis.py.
Traceback (most recent call last):
…
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Several notebooks do trajectory visualization with `nglview`; it would be helpful to migrate those to something which will work on Colab. The most important seem to be:
- MD sandbox on molecules
- S…
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Hi!
I was reading the SaLSA paper, and it appears clear that the non-locality of the model is done through the "nonlocal “spherically averaged liquid susceptibility” in equation 5 (image)
![imag…
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From @hmacdope on Discord:
Create a directory with Jupyter notebooks that have examples + detailed explanations
Good reference: https://github.com/MDAnalysis/solvation-analysis/blob/main/docs/tu…
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If you run `transrate` in Ubuntu 16.04 and have problems like follow when run `salmon(0.6.0)`
```
./salmon: relocation error: /tools/transrate-1.0.3-linux-x86_64/bin/librt.so.1: symbol __vdso_clock…
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I've noticed the new OpenMM 8 solvation algorithm appears to give very large box sizes for complex and possibly too-small box sizes for solvent:
![image](https://user-images.githubusercontent.com/365…
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Hi,
I'm enjoying using the QCG modules, and in addition to having some successful outcomes, I've run into an issue for long, "linear" molecules. The process begins by placing the first solvation l…
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Dear developers,
I find some new features have been released without updating the documents.
1. Implicit Solvation
all available solvents have been extended to GFN-FF method since…
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Dear developers:
As shown in the question, I performed constant potential simulation calculations in Vaspsol++using the README method. However, when I added the following parameters to INCAR, …
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I'm trying to run
mdpow-equilibrium --solvent octanol glyh101.yml
I did the same with --solvent water and had no issues.
I copied the runinput.yml from the templates and made a few changes (copi…