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[BUG] The intrascale matrix read by the AmberPrm parser disagrees with the saved one for perturbable systems #213

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lohedges opened this issue Dec 1, 2023 · 0 comments · Fixed by #210
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[BUG] The intrascale matrix read by the AmberPrm parser disagrees with the saved one for perturbable systems #213

lohedges opened this issue Dec 1, 2023 · 0 comments · Fixed by #210
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lohedges commented Dec 1, 2023

I'm not yet sure if this a general issue with the sire.legacy.IO.AmberPrm parser, or is a specific problem for perturbable systems, but the intrascale matrix loaded via readPerturbableMolecules doesn't agree with the one of the perturbable molecule that was saved in either end state. This is causing issues when running simulations with somd2. For now, a workaround is to regenerate the matrix using the sire.legacy.IO.GroTop parser.
@lohedges lohedges added the bug Something isn't working label Dec 1, 2023
@lohedges lohedges self-assigned this Dec 1, 2023
lohedges added a commit that referenced this issue Dec 1, 2023
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Reconstruct intrascale matrices using the GroTop parser. [closes #213]
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@lohedges lohedges mentioned this issue Dec 1, 2023
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Fix #208 OpenBioSim/biosimspace
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