Feature restraint #105
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Feature restraint #105
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…ll let you easily get energies for different lambda values, plus control lambda in a simulation. As part of this, I have also updated the minimisation interface to inherit from dynamics (so that you can minimise at different lambdas) I have also ported in the new updateProperty code, adding a convenience function to MolEditor so that the openmm interface can copy across coordinates while minimising allocation and deallocation of memory
…trajectory. This includes passing in lambda windows so that energies for different lambda values can also be saved. Also updated the code that extracts coordinates and velocies to use the faster updatePropertyFrom function.
…on arguments. Have these automatically convert to units from strings
…uring a dynamics simulation. This can be nicely output as a pandas dataframe for further processing
…l metadata, plus to have a null pointer if the Properties is empty. This should save some memory (given that metadata is almost never used) plus should speed things up a little as there is no need to allocate shared data for empty Properties objects.
…nks to properties
so that they can be accessed via alternate names. This is mainly useful for
merged molecules, e.g.
```
>>> mol = mols[0].edit().add_link("coordinates", "coordinates0").commit()
>>> mol.view()
```
would let the `coordinates0` property be used as `coordinates` when
viewing the molecule (or any other place that `coordinates`
was needed)
…when it changes like this
…ctions. Added default LambdaSchedule if it is not set, plus added convenience functions that make it easier to create standard types of schedule. Fixed some bugs. Can now run free energy simulations for solvated ethane->methanol :-)
…n reality, I won't, instead relying on people minimising the system properly before running. I will update the constraints for perturbable molecules to be based on the actual coordinates of the atoms, rather than forcefield parameters
…mass of the perturbing atoms so that automatically applied constraints apply equally to both sides of the perturbation. This is important because internals that are constrained don't have their energy evaluated.
…jectories. An empty one is now created if you ask for one. Also fixed a bug in Dynamics that meant that the time in the EnergyTrajectory was the current simulation time, not the overall simulation time.
…bed internals. The code was accidentally pulling internals from the perturbed state multiple times. This fixes that bug, and adds a more complex merged molecule to the tests (zanamivir to oseltamivir) I've also updated the lever so that it can cope with missing forcefields. This will make debugging easier :-)
…ions to or from ghost atoms into custom ghost forcefields. The custom forcefield is currently just a copy of the LJ potential, but it will eventually become more complex once I've double-checked all the bookkeeping. I am currently missing a small forcefield to handle the 1-4 nonbonded interactions involving ghost atoms. Suspiciously though, the energies are correct... (which more likely signals a bug)
…aLever ;-) To make the bookkeeping easier, and avoid the expensive search over ALL exceptions in the CLJFF, I am now handling all of the exceptions for perturbable molecules manually, using the ExcludedPairs object. This lets me find the 1-4 terms involving ghost atoms more easily, and also identify and manipulate them using the lever. This is currently broken though, as I haven't excluded everything that needs excluding... Will try again another time ;-) WIP
…LJFF. This is to re-use the information that sire already has, and to also make it easier to put the full set of exceptions (with scale factors) into OpenMMMolecule. This will also make it easier to perturb these scale factors, which will be needed once we support bond breaking / making in a perturbation.
… involving ghost atoms. These now give the correct energy. The code is a little slow to now create the context (1-3 seconds) - I think because it is going over all intra-atomic pairs. I will need to explore some optimisations.
… speeds things up a bit, as we now don't need to build a large exceptions list and feed it serially to openmm. We only fully manage the exceptions ourselves for perturbable molecules.
…maps when updating coordinates / velocities. This is needed so that the results of one stage (e.g. minimisation) go back into the right property for the next stage for that perturbable molecule (e.g. the minimised coordinates go into `coordinates0` rather than `coordinates` for the perturbable molecules)
and control perturbations, e.g.
```
>>> import sire as sr
>>> mols = sr.load_test_files("merged_ligand.s3")
>>> mols.perturbation().view()
```
will view the perturbation as a movie in a jupyter notebook.
There is an option to shrink ghost atoms. This will pull these atoms
inside their connected atoms as they become ghosts.
The animation looks cool, and really helps visualise what is happening
across lambda. I just need to find a way to control the colors / sizes
of the atoms in nglview, plus also specify the bonding myself rather
than having nglview work it out automatically.
…morph` module. Broken out the functionality to shrink ghost atoms to a new `shrink_ghost_atoms` function. Initial testing suggests that 0.6 A is a reasonable default length (shrinks without leading to NaN errors) Added soft core LJ potential, using a per-atom shift_delta parameter that will be scaled with lambda :-) Added this to both the CLJ force and NB14 force.
…have full LJ and coulomb softening, which seems to work well. Added option to `SOMMContext` to return energies in sire units. This is switched on by default, as I have surprised myself too many times with units errors ;-)
…venience arguments, plus better API docs
…e found Updated the changelog so that it matches the upcoming 2023.3.2 release Merged in all changes from `main`
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… exchange moves between `sire.mol.Dynamics` objects. This is general replica exchange, allowing changes in lambda, temperature or pressure between replicas. Moved all of the minimisation functionality into `DynamicsData` and added a `minimise()` function to `Dynamics`. This makes it easier to add minimisation into a dynamics run, without having to create a new context. Also makes it easier to add minimisation to the beginning of lambda replica runs.
…l let you change the temperature or pressure of a running dynamics simulation. This will cause a NotImplementedError though, as I haven't yet added the function to change the temperature or pressure in the integrator, nor rescale the velocities if that is desired.
… when shared properties are off. Also fixed a streaming bug in Frame
…s to give a better-shaped PMF for ethane to methanol
Changed this to a length so we are not a factor of 10 out in the OpenMM code!
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…d api. Fixed issue where a System has a space, but it isn't shared, meaning that it is lost when the System is converted to OpenMM
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From the changelog:
Added support for restraints to the OpenMM dynamics layer. Initial tested
support for positional and distance/bond restraints is included, as well
as experimental support for Boresch restraints. The restraint are documented
in the :doc:
tutorial <tutorial/part06/03_restraints>. This also documentsnew code to let you specify atoms that should be fixed in space.
Added support for alchemical restraints to the OpenMM dynamics layer.
This lets you scale restraints as part of a λ-coordinate. This is
documented in the :doc:
tutorial <tutorial/part06/04_alchemical_restraints.Restraints can be named, meaning that you can scale different restraints
at different stages and by different values across the λ-coordinate.
This is tested in
tests/convert/test_openmm_restraints.py. The extra options added to the OpenMM layer are also documented in the cheatsheet,doc/source/cheatsheet/openmm.rst.develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@lohedges, @mb2055
Any additional context of information?
This PR builds on and supersedes
feature_soft.I still need to write the tutorial for the general lambda lever and general perturbation. I will do this as part of the last of the three stages of this grand PR,
feature_bond_breaking, when I will add support for ring-breaking perturbations.