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Error Running #2

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JessBoette opened this issue Jun 23, 2023 · 1 comment
Open

Error Running #2

JessBoette opened this issue Jun 23, 2023 · 1 comment

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@JessBoette
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Trying to run the compute_bulk.py using trajectory and topology from SI: https://zenodo.org/record/6478270

Keep running into error in the find_offsets function. In L79 the function needs a parameter "d" that is missing in the code. I'm not sure what the idea parameter and settings should be.

Thanks in advance!
@klyshko
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klyshko commented Jul 26, 2023 •
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Hi @JessBoette, thanks for your question.

Parameter d in the find_offsets() function is a distance matrix dist_mtx between the coordinates of bulk WS and all water oxygens in the system. Make sure that the dist_mtx calculated in L68 is not empty.

Let me know if you have other questions.

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@klyshko @JessBoette