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Add OpenMM module #482
Add OpenMM module #482
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The code presented in this commit was enterily done by Ivar de Leeuw during his Master course: Major Research Project (GSLS), academic year 2021-2022. I am pushing the code after Ivar's request and in its exact original form. In the next commits, the team will work on Ivar's code to accommodate it fully to the HADDOCK3 project. Thanks Ivar for all your great work and best luck on your future studies!
Made a general linting around files. Addition lint can still be done on function and variable names. |
Hi @joaomcteixeira, just had a quick chat with Ivar De Leeuw about the version of the dependencies he used: it's openmm v. 7.7.0 and pdbfixer 1.8.1. I'll modify the INSTALL.md accordingly |
Okay. I strongly suggest having them defined as optional dependencies, same as lightdock and gdock. |
I totally agree. |
tried a run with the example file
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I would say this is not ours and is something from |
@mgiulini, the pre-last commit solves the Also corrected some defaults that were lists to single strings |
Undo linting from all previous commits. After linting, some deep bug appeared and I found no way to reproduce the original results. So, we need to lint block by block very carefully. I left the other files: install.md and config_read untouched because those changes will surely go through.
As for the reproducibility: it is possible to assign a seed to the integrators, but not to the modeller functions. Therefore, the solvation boxes specified at the beginning of the simulations are bound to differ. |
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lgtm
Co-authored-by: Anna Engel <113177776+AljaLEngel@users.noreply.github.com>
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What will happen if a protein-ligand complex is passed to the openmm module?
Is there a check that only "pure" protein and nuclei acids are accepted?
Also I assume (did not check the openmm code) that the system is neutralised by adding counter ions. Is this true?
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Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>
7253d32
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The code presented in this commit was entirely done by Ivar de Leeuw during his Master course: Major Research Project (GSLS), academic year 2021-2022.
I am pushing the code after Ivar's request and in its exact original form.
In the next commits, the team will work on Ivar's code to accommodate it fully to the HADDOCK3 project.
Thanks, Ivar, for all your great work and best luck with your future studies!