Code

Feature bond breaking#111

Code

Merged

chryswoods merged 45 commits intodevelOpenBioSim/sire:develfrom feature_bond_breakingOpenBioSim/sire:feature_bond_breakingCopy head branch name to clipboardOct 10, 2023

+4,125-578

Commits

Commits on Sep 19, 2023

• Added support for using the Andersen thermostat instead of an integrator

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  chryswoods

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  af04346

Commits on Sep 20, 2023

• Added the intramolecular scale factors to the LambdaLever. This should mean that we

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• I've moved the messiness of the perturbable parts of OpenMMMolecule into a more user-friendly

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  chryswoods

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  d9cd2ad

Commits on Sep 21, 2023

• Working on the tutorial, filling in missing or confusing functionality as needed

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• Continuing to work on the tutorial

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• Finished writing the tutorial docs for the new perturbation code. All that's needed now

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Commits on Sep 22, 2023

• Working on a way to get energy trajectory output that is more compatible with alchemlyb

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• Made sure that we match dihedrals by atoms AND periodicity, so that we don't

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Commits on Sep 26, 2023

• Fixed printout of the temperature of an ensemble

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• Updated EnergyTrajectory so that it can output labels as numbers, and also

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• Working on the free energy simulation tutorial page. This shows how to run a simple free energy

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• Quick note that we don't really need parquet

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Commits on Sep 27, 2023

• Make sure that we don't record energies / frames when the update frequency is set to zero.

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Commits on Sep 28, 2023

• I've finished off the tutorial on calculating and analysing free energies.

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• Fixed some small typos in the tutorial

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Commits on Oct 1, 2023

• Added an option to constrain the perturbable molecules using a different constraint method

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Commits on Oct 2, 2023

• I've added a sire.morph.repartition_hydrogen_masses function (with unit test)

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• Added functions to let the user easily set the temperature and/or pressure, and also to

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Commits on Oct 3, 2023

• Switched repartition_hydrogen_masses over to using the C++ function

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  Christopher Woods

  authored and

  Christopher Woods

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• Continuing to work on the tutorial...

  

  Christopher Woods

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  Christopher Woods

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• Still working on the last part of the tutorial.

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Commits on Oct 4, 2023

• Added the option to control whether or not the internal energy/forces of constrained

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  Christopher Woods

  authored and

  Christopher Woods

  committed
  fae4597

Commits on Oct 5, 2023

• Need to make sure that HMR repartitions the masses in both end states, or else it is ignored...

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  chryswoods

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• Working on speeding things up

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Commits on Oct 6, 2023

• Added the ability to store the ensemble (and thus temperature) in the EnergyTrajectory.

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• I've changed the default hydrogen mass repartitioning (HMR) factor from 4 to 1.5,

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• Fixed some typos and added the results of running the script to the end of the tutorial.

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Commits on Oct 7, 2023

• Finished the free energy tutorial with the results from the long simulation run.

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• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_bond_breaking

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• Updated the changelog. Added the pentane to cyclopentane test, and already have an error :-)

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• Merge branch 'feature_tag_build' of https://github.com/openbiosim/sire into feature_bond_breaking

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• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_bond_breaking

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• Small corrections

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• Got the bond-breaking molecule to load into OpenMM by realising that I don't need

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• Fixed the typo-bug in openmmmolecule.cpp that was stopping bond breaking from working.

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• I think this fixes the compile error on Windows (missing definition of PhysUnit(GeneralUnit) constructor,

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• Website-only updates. Updated the changelog, added free energy to the features and

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• Possible fix for the windows link error.

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• Need to add back this header file to compile on MacOS

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• Another Windows compile fix. I think these have all come up because boost has updated to

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• Fix needed for Linux...

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Commits on Oct 8, 2023

• Disabling unsupported tests on windows

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• Copilot got that wrong...

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• Cleaning up the website ready for the release. Moved the blog posts into their own

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Commits on Oct 9, 2023

• Dynamics.energy_trajectory should not default to the pandas output

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