Feature Permanent Distance Restraints #110
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This allows the use of "permanent" distance restraints which are always at full strength, even in "turn on receptor-ligand restraints mode". This allows multiple distance restraint protocols which involve turning off some distance restraints without affecting others.
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Is this pull request to fix a bug, or to introduce new functionality?
This PR adds support for one or more "permanent" distance restraints. These are distance restraints that are always applied, and are never scaled by λ. This allows the release of all other distance restraints to a single harmonic or flat-bottomed restraint. When the ligand is fully decoupled, the free energy of release of the single remaining restraint can be computed without simulation. This provides more options for using multiple distance restraints in ABFE calculations.
I will create a parallel PR to BioSimSpace with functionality for setting up and running ABFE calculations in this way.
If this introduces new functionality...
Changes proposed in this pull request:
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): yI haven't yet added new tests as I was unsure how best to do this. Ideally, I would add some tests similar to this. Would a test like this be too slow? What would you recommend?
Suggested reviewers:
@chryswoods, @lohedges
Any additional context of information?
I'm currently testing SOMD ABFE calculations with Boresch restraints against multiple distance restraints as shown here. Both methods produce results which are statistically indistinguishable with the TYK2 system tested:
Thanks very much.