choderalab/pymbar issues and pull requests

#542 - Switch from u_kln to u_kn in examples

Issue - State: open - Opened by mrshirts 10 days ago

#541 - Issue docstring harmonic

Pull Request - State: open - Opened by jaclark5 10 days ago - 6 comments

#540 - Enthalpic and Entropic Contributions from BAR

Pull Request - State: closed - Opened by jaclark5 10 days ago - 14 comments

#539 - Use self.u_kn when verbose=True in MBAR

Pull Request - State: closed - Opened by jaclark5 about 1 month ago - 5 comments

#538 - Verbose=True with MBAR results in an error for alternative input types of u_kn

Issue - State: closed - Opened by jaclark5 about 1 month ago

#537 - Issue gitignore

Pull Request - State: closed - Opened by jaclark5 about 1 month ago - 1 comment

#536 - Examples output pdfs are listed in untracked files

Issue - State: closed - Opened by jaclark5 about 1 month ago - 3 comments

#535 - Fix to bootstrap of free energy surfaces, affecting timing and quantitative results

Pull Request - State: open - Opened by mrshirts about 1 month ago - 5 comments

#534 - Reduced Potential Definition in pymbar's FES Implementation

Issue - State: open - Opened by joaco-rgb 3 months ago

#533 - Issue calculating FES from umbrella sampling with CV between protein C-term and N-term

Issue - State: open - Opened by Byun-jinyoung 3 months ago

#532 - Fast way of computing the MBAR analytical error

Issue - State: open - Opened by xiki-tempula 3 months ago

#531 - Unreasonable fes.generate_fes KeyError

Issue - State: open - Opened by cecilia-hong 4 months ago - 5 comments

#530 - robust method won't work with verbose=True

Issue - State: open - Opened by xiki-tempula 5 months ago - 10 comments
Labels: bug

#529 - Revising the conda release strategy

Issue - State: open - Opened by xiki-tempula 5 months ago - 2 comments

#528 - Key error due to high nbins

Issue - State: open - Opened by ashiquelal 5 months ago

#527 - fix minor typos

Pull Request - State: closed - Opened by schuhmc 6 months ago

#526 - Update to Python 3.12

Pull Request - State: closed - Opened by Lnaden 6 months ago - 2 comments

#525 - Would using pymbar's autocorrelation module be useful in reducing the number of simulations required when running non-eq FEP?

Issue - State: open - Opened by DreamCykl 7 months ago

#524 - Support newer jax version (0.4.25) where jax.config.config is removed.

Pull Request - State: closed - Opened by nielskm 7 months ago - 1 comment

#523 - BAR estimate without overlap

Issue - State: closed - Opened by wiederm 7 months ago - 2 comments

#522 - Shrink the overlap matrix for a subset of lambdas

Issue - State: closed - Opened by xiki-tempula 8 months ago

#521 - NameError: name 'ConvergenceError' is not defined

Issue - State: open - Opened by PhilippHoellmer 8 months ago

#520 - [Q] intrinsic difficulty when solving MBAR for large number of similar thermodynamic states

Issue - State: open - Opened by svandenhaute 8 months ago

#519 - MBAR gives a statistical error magnitudes larger than the bootstrap error.

Issue - State: open - Opened by xiki-tempula 9 months ago - 4 comments

#517 - Assorted maintenance updates

Pull Request - State: open - Opened by mattwthompson 11 months ago - 2 comments

#516 - Support Python 3.12

Pull Request - State: closed - Opened by mattwthompson 11 months ago - 1 comment

#515 - solver_protocol: "continuation = True" does not exhibit the desired effect? (bug vs. misunderstanding?)

Issue - State: open - Opened by denisdertli 11 months ago

#514 - Questions on `compute_expectations`

Issue - State: open - Opened by gooaah 12 months ago - 2 comments

#513 - Fixed example bug and updated output.

Pull Request - State: closed - Opened by mrshirts about 1 year ago - 4 comments

#512 - Fix a small bug in the timeseries test, test against min and max versions

Pull Request - State: closed - Opened by Lnaden about 1 year ago - 1 comment

#511 - FES incorrectly assigns samples larger than bin bounds, also does not handle empty bins correctly

Issue - State: open - Opened by Lnaden over 1 year ago - 1 comment

#510 - fixes RTD build

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#509 - Make using JAX (or any accelerator) an Instanced Python class (and toggle)

Pull Request - State: open - Opened by Lnaden over 1 year ago - 4 comments

#508 - Make using JAX (or any accelerator) a toggle

Pull Request - State: closed - Opened by Lnaden over 1 year ago - 7 comments

#507 - Correct docstring default value

Pull Request - State: closed - Opened by badisa over 1 year ago - 1 comment

#506 - Wrap the preconditioned jit

Pull Request - State: closed - Opened by Lnaden over 1 year ago - 1 comment

#505 - Correctly stagger JIT until first call

Pull Request - State: closed - Opened by Lnaden over 1 year ago - 1 comment

#504 - Warn about JAX bitsize changes

Pull Request - State: closed - Opened by Lnaden over 1 year ago - 1 comment

#503 - Make JAX an optional dependency

Pull Request - State: closed - Opened by Lnaden over 1 year ago - 2 comments

#502 - [DNM] Update fes.py (BUG!)

Pull Request - State: closed - Opened by rosadche over 1 year ago - 4 comments

#501 - pip seems to not be so happy with JAX

Issue - State: open - Opened by xiki-tempula over 1 year ago - 1 comment

#500 - Optional JAX dependency

Issue - State: closed - Opened by Lnaden over 1 year ago - 30 comments

#499 - mini-batch based solver?

Issue - State: open - Opened by mrshirts over 1 year ago
Labels: enhancement, pymbar 5

#498 - Catch the issue of not being able to find ptxas

Issue - State: open - Opened by xiki-tempula over 1 year ago - 1 comment
Labels: bug, documentation, pymbar 4

#497 - see if tests pass without 64 bit floats

Pull Request - State: open - Opened by mikemhenry over 1 year ago - 1 comment

#496 - Silently changing JAX default config

Issue - State: open - Opened by invemichele over 1 year ago - 10 comments
Labels: bug, pymbar 4

#495 - use mamba to build docs on the lts branch

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#494 - switch to using mamba for rtd building

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 3 comments

#493 - readthdocs not building; looks like config issue

Issue - State: closed - Opened by mrshirts over 1 year ago - 4 comments

#492 - Minor docstring exp fix

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 3 comments

#490 - MBAR uncertainty estimates in a low-overlap case

Issue - State: open - Opened by maxentile over 1 year ago - 2 comments

#489 - Check outputs.

Issue - State: open - Opened by mrshirts over 1 year ago

#488 - jax initialization issues

Issue - State: open - Opened by mrshirts over 1 year ago - 5 comments

#485 - Do not use removed `numpy.bool`

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments

#484 - Examples do not work with NumPy 1.24

Issue - State: open - Opened by mattwthompson almost 2 years ago - 5 comments

#483 - Problem with parallel-tempering-2dpmf.py

Issue - State: closed - Opened by francoviscarra almost 2 years ago - 1 comment

#482 - Add bootstrap_solver_tolerance argument

Pull Request - State: closed - Opened by zhang-ivy almost 2 years ago - 1 comment

#481 - Separate solver tolerance for bootstrapping

Pull Request - State: closed - Opened by zhang-ivy almost 2 years ago

#480 - Revert "allow separate bootstrap_solver_tolerance arg"

Pull Request - State: closed - Opened by mikemhenry almost 2 years ago

#479 - The discrepancy in calculating u_kln between parallel-tempering-2dpmf.py and umbrella-sampling.py

Issue - State: open - Opened by Vinvin-Zhang almost 2 years ago - 1 comment

#478 - create unique bin values

Pull Request - State: open - Opened by shawnhsueh almost 2 years ago - 2 comments

#477 - bin value are not unique

Issue - State: open - Opened by shawnhsueh almost 2 years ago - 3 comments
Labels: enhancement

#476 - bin_edges in multi-dimension PMF can only have equal number of element in each dimension

Issue - State: open - Opened by shawnhsueh almost 2 years ago - 3 comments
Labels: question

#475 - pymbar 3.1 release not available through PyPI

Issue - State: closed - Opened by boegel almost 2 years ago - 1 comment

#474 - linux-aarch64 conda support?

Issue - State: open - Opened by jmichel80 about 2 years ago - 4 comments

#472 - Mapping old `method` argument to new API

Issue - State: open - Opened by mattwthompson about 2 years ago - 3 comments
Labels: pymbar 4

#471 - sphinx.ext.pngmath is now sphinx.ext.imgmath

Pull Request - State: closed - Opened by mikemhenry about 2 years ago - 3 comments
Labels: pymbar-3-lts

#470 - Fix divide by zero warning in pymbar3

Pull Request - State: closed - Opened by zhang-ivy about 2 years ago - 7 comments
Labels: pymbar-3-lts

#469 - Cleanup and fixing for a 4.1 release.

Issue - State: open - Opened by mrshirts about 2 years ago