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openmm-ml compatibility for generic MultiStateSampler objects #598

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openmm-ml compatibility for generic MultiStateSampler objects #598

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dominicrufa
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@dominicrufa dominicrufa commented Jul 6, 2022 •
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Description

implement compatibility for openmm-ml (and openmm 8/beta) to allow for generic MultiStateSampler free energy/sampling calculations.

Todos

  • Implement feature / fix bug
  • Add tests
  • Update documentation as needed
  • Update changelogNotable points that this PR has either accomplished or will accomplish.

Status

  • Ready to go

dominicrufa and others added 25 commits July 6, 2022 13:29
@dominicrufa
stage nnp alchemical state
6aa8955
@dominicrufa
add openmm-compatible mixin
93e16ae
@dominicrufa
fix NNPProtocol import
3ad05a6
@dominicrufa
fix import
2195115
@dominicrufa
Merge branch 'choderalab:main' into ommml_compat
b1a5b86
@dominicrufa
removing minimization args since we outside of constructor
4d4bf43
@dominicrufa
Merge branch 'ommml_compat' of https://github.com/dominicrufa/openmmt…
0a3f7e2 
…ools into ommml_compat

rebasing from `openmmtools` `main` update
@dominicrufa
add user-side hybrid mm/ml repex constructor
dd18270
@dominicrufa
make more robust storage and add __init__.py
2dbdbd5
@dominicrufa
default to
9c2443e
@dominicrufa
add auxiliary kwargs for createMixedSystem
9383583
@dominicrufa
allow replica independent dynamics
b2df1e7
@dominicrufa
remove independent replicas
b366728
@dominicrufa
Merge branch 'choderalab:main' into ommml_compat
24100a1
@dominicrufa
Merge branch 'ommml_compat' of https://github.com/dominicrufa/openmmt…
254e9b8 
…ools into ommml_compat

sync fork
@dominicrufa
removing unused kwarg
489dd00
@dominicrufa
Merge branch 'choderalab:main' into ommml_compat
93d186a
@dominicrufa
run repex corrections for omm8
ffffe8f
attempt a gentle annealing protocol to seed replica exchange
ef9f6ab
@dominicrufa
Merge pull request #1 from dominicrufa/origin/ommml_compat
3a08d42 
attempt a gentle annealing protocol to seed replica exchange
@dominicrufa
add printing logger and fixed for gentle equil
a34c0f1
@dominicrufa
make final state endstate in lieu of restraints
9685995
@dominicrufa
add verbosity and prints
b559f9c
@dominicrufa
add protocol and register for lambda_interREST
60be483
@dominicrufa
revert to orig rest implementation
8def71d
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codecov bot commented Jun 26, 2023 •
edited

Codecov Report

Merging #598 (389531b) into main (b379af3) will decrease coverage by 0.56%.
The diff coverage is 14.60%.

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