Skip to content

openmm-ml compatibility for generic MultiStateSampler objects #598

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
dominicrufa wants to merge 27 commits into
base: main
Choose a base branch
from
Open

openmm-ml compatibility for generic MultiStateSampler objects #598

dominicrufa wants to merge 27 commits into from

Conversation

@dominicrufa
Copy link
Contributor

@dominicrufa dominicrufa commented Jul 6, 2022 •
edited
Loading

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

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

sync fork
removing unused kwarg
489dd00
@dominicrufa
Merge branch 'choderalab:main' into ommml_compat
93d186a
run repex corrections for omm8
ffffe8f
@dominicrufa
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
add printing logger and fixed for gentle equil
a34c0f1
make final state endstate in lieu of restraints
9685995
add verbosity and prints
b559f9c
add protocol and register for lambda_interREST
60be483
revert to orig rest implementation
8def71d
@codecov
Copy link

codecov bot commented Jun 26, 2023 •
edited
Loading

Codecov Report

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

1 participant

@dominicrufa