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OpenBioSim / sire

Sire Molecular Simulations Framework
https://sire.openbiosim.org
GNU General Public License v3.0
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Add "auto" constraints and then update tutorial #185

Closed chryswoods closed 6 months ago

chryswoods commented 7 months ago

Matching the constraints algorithm in somd has been fun... In that discussion the concept of auto constraints based on vibrational frequencies of bonds (i.e. as in gromacs) has been suggested. I'm adding this issue as a reminder to implement this for the next major release.

As part of this, we need to update the constraints chapter of the tutorial, and also our suggestions for best practice. These are falling increasingly out of date given our implementation of dynamic constraints, and the new -not-perturbed constraint variants.

Additional context This is a placeholder for the constraints work for the 2024.2.0 release.

chryswoods commented 7 months ago

I made a feature branch to implement this, but accidentally put this in feature_merge2. Since it was quick to implement, and doesn't impact existing functionality, I've decided to leave it in feature_merge2 and include it in 2024.1.0.

I will update the constraints chapter of the tutorial in a separate branch which I will include as part of the release (I don't want to keep changing feature_merge2 while it is being tested - it really is finished now)