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Update default hydrogen mass to 3 amu for protein mutations #982

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zhang-ivy opened this issue Apr 12, 2022 · 0 comments · Fixed by #983
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Update default hydrogen mass to 3 amu for protein mutations #982

zhang-ivy opened this issue Apr 12, 2022 · 0 comments · Fixed by #983
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0.10.0 Enhanced C...

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zhang-ivy commented Apr 12, 2022 •
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Using 4 amu causes stochastic nans for some transformations, e.g. ALA->TYR where hydrogen mass repartitioning with 4 amu causes the CB to have a mass of 4.53 amu and each of the HBs have a mass of 4 amu, which leads to instabilities, particularly when running with rest over the protocol.
Note that this has already been done for small molecules.
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Change default hydrogen mass choderalab/perses
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