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Element goes assigned incorrectly during gmx dihedral optimisation #35

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xiki-tempula opened this issue Jan 21, 2022 · 2 comments
Closed

Element goes assigned incorrectly during gmx dihedral optimisation #35

xiki-tempula opened this issue Jan 21, 2022 · 2 comments

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@xiki-tempula
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I have a test molecule.
start.xyz
image
Which will give a fragment to be optimised
start_qforce/fragments/CC_H8C8O1_b5c19484a341b9ee3378be1f8a23bc522.out
image
The QM calculation runs fine but when fitting the dihedral through gmx, it will optimise the wrong fragment.
start_qforce/fragments/CC_H8C8O1_b5c19484a341b9ee3378be1f8a23bc522/step23/em.gro
image
Note the wrong nitrogen.

Please find all the files attached.
Archive.zip
@selimsami
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Here the atom type should be Hydrogen still. So it's only a visualization issue.

@xiki-tempula
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@selimsami Thank you. It seems to be a charge issue which I have discussed in #36.
Thus, I closed this issue.

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@xiki-tempula @selimsami