Fix 116 #117
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Fix 116 #117
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…by comparing the measured distance against either r0 (for bonds) or a list of seen angle distances for angles. This massively speeds up OpenMM, as it is now able to find equivalent molecules and optimise itself internally.
…ons" error in 8.1beta, but only when the bonds(!?) change. The fix is to minimise with h-bond constraints turned on. I've added a note about this to investigate later, and updated the docs and example script to minimise with h-bonds (with perturbable_constraint='none' as otherwise that defeats the point of minimising...)
… the minimisation process (i.e. correcting issues caused by our use of custom forcefields for perturbations) Will eventually integrate with the progress bar system plus give more control over the way that constraints are handled
…reporting via the ProgressBar class.
Fixed exclusions/exceptions errors on the CPU platform
…cules with no internal bonding. Added a better algorithm to detect and fix this. Also cleaned up the code to get a shared constraint length. Added the changelog entries ready for the PR
compliant. Also, the tests give about 97% coverage :-)
…stake was that I had replaced ``` if type(C) != D: ``` with ``` if isinstance(C, D): ``` when it should have been ``` if not isinstance(C, D): ``` All fixed now. Does not need a CI rebuild. [ci skip]
This (hopefully) will fix the issue?
…of dynamics/minimisation adding in a fake OpenMM box when vacuum systems are committed
lohedges
approved these changes
Oct 23, 2023
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All BioSimSpace tests are passing and the somd2 minimisation issue is resolved. The one thing to note is that tests/convert/test_openmm_minimise.py appears to pass both before and after the fix. I'm not sure why this system isn't affected by the issue that I was seeing. Perhaps it's worth updating the test with the perturbable molecule example so that we know we're using something that used to fail.
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This pull request fixes issue #116 and also fixes the vacuum bug reported on slack.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@lohedges
Any additional context of information?
This builds on and supersedes PR #114