Automated solvation shell extraction workflow #8
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levineds
reviewed
Apr 25, 2024
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On another note, where should we be tracking pip/conda package dependencies for this code? |
levineds
reviewed
May 15, 2024
I think that goes in om-data/setup.py (i.e. the setup.py in the parent directory) |
jeevster
commented
May 15, 2024
| lattices = np.array([a, b, c])[None][None] | ||
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| # Choose solute atom | ||
| solu = universe.select_atoms(f"name {solute_atom}") |
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Also, I realized that this doesn't yet support multiple atoms in a single solute. I'll get on this.
levineds
reviewed
May 16, 2024
added 7 commits
May 16, 2024 17:11
…ng pipeline, need to test
… solute and solvent resname dictionary construction
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In this PR, we construct a workflow for extracting diverse solvation shells from MD trajectories of electrolyte systems. This workflow operates on PDB files and outputs a directory containing xyz files organized according to solute type and coordination number.
Note: for low-concentration simulations, this workflow is likely sufficient for extracting the solvation shells we require. However, for high concentration simulations, we will need to do a network/topology analysis to extract more interesting snapshots. This will be completed in a future PR.