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Consistent indices in PyGromos #299

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pultar opened this issue Aug 5, 2022 · 0 comments
Open

Consistent indices in PyGromos #299

pultar opened this issue Aug 5, 2022 · 0 comments
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cleaning this contains cleaning of stuff documentation Improvements or additions to documentation

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@pultar
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pultar commented Aug 5, 2022

GROMOS starts counting from "1" in topologies (and other places). However, sometimes atom indices are 0 indexed (for example functions that use mdtraj). We should make this more consistent before too many people use functions.

I think we should stick to GROMOS convention and start everywhere from "1".

@MTLehner ideas?
@pultar pultar added documentation Improvements or additions to documentation cleaning this contains cleaning of stuff labels Aug 5, 2022
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