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I am trying to calculate free energies of binding with Yank between a protease and a short peptide sequence. I initially tried setting up the system with the ligand specified via a pdb file. I realize…
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Hi, I recently started trying this repo and found it really cool!
I have managed to run the example in `examples/example_scripts/train_model/` on some data and would like to use the final model to e…
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@mrshirts I am trying to modify the code so that it can handle multiple references. In other words, say we start with TraPPE and get a new optimal with lambda = 14. Then we do direct simulation of thi…
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Currently we have a mismatch where we have some details about how solvation happens in the SolvationSettings and some in SolventComponent.
My proposal is that **anything that defines the molecular …
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I tried using this code to generate the potential energy curve for the CF molecule and I got this error message: …
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Ok the tests seemed to work on my laptop, so I moved to a workstation to process the full dataset overnight. I updated sire to the latest devel branch and then launched the test script.
```
[ ju…
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![image](https://github.com/StructuralGenomicsConsortium/CNP16-iminoquinone-SarsRdRp-mechanstic-study/assets/147162201/e6026512-a8e3-4727-8db1-d1c955dba7aa)
In this project, we think we've seen an …
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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…
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Hi developers,
First of all, I would like to thank the developers who released the CASM code. I recently wanted to do some research on disordered rocksalt using CASM code and have the following que…
ghost updated
2 years ago
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The INI file doesn't match any convention I recognise and is quite hard to read. There are better config handlers that do the parsing and loading for free. Here is an example TOML config file that I w…