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Charge in consistency between the files in gromacs_solvated.tar.gz and gromacs.tar.gz #53

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dingye18 opened this issue Nov 19, 2024 · 0 comments

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@dingye18
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I just found that that atomic charges of part of the molecules are different in gromacs_solvated.tar.gz and gromacs.tar.gz.
Such as the mobley_820789, the atomic charges in gromacs/mobley_820789.top are:
image

While in gromacs_solvated/mobley_820789.top:
image
That's quite different. And only the parameters in gromacs/mobley_820789.top can reproduce the result in literature.
Openff-toolkit was used to regenerate the atomic charges of mobley_820789 with gaff-1.8, and the regenerated charges were consistent with the content in gromacs/mobley_820789.top.

How did the charges in gromacs_solvated generated? And was it processed after gaff-1.7?

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