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selimsami / qforce

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Element goes assigned incorrectly during gmx dihedral optimisation #35

Closed xiki-tempula closed 2 years ago

xiki-tempula commented 2 years ago

I have a test molecule. start.xyz image Which will give a fragment to be optimised start_qforce/fragments/CC_H8C8O1_b5c19484a341b9ee3378be1f8a23bc52~2.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_b5c19484a341b9ee3378be1f8a23bc52~2/step23/em.gro image Note the wrong nitrogen.

Please find all the files attached. Archive.zip

selimsami commented 2 years ago

Here the atom type should be Hydrogen still. So it's only a visualization issue.

xiki-tempula commented 2 years ago

@selimsami Thank you. It seems to be a charge issue which I have discussed in https://github.com/selimsami/qforce/issues/36. Thus, I closed this issue.