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Issues list

Better default behavior for failure/success of MBAR solver.
#548 opened Feb 26, 2025 by mrshirts updated Feb 26, 2025
@mrshirts
Add bootstrap to EXP and BAR? enhancement
#546 opened Dec 27, 2024 by mrshirts updated Dec 27, 2024
@mrshirts
Including methods for equilibration detection
#543 opened Oct 21, 2024 by ijpulidos updated Dec 2, 2024
6
Should Subsampling be Recommended?
#545 opened Nov 18, 2024 by fjclark updated Nov 21, 2024
2
hybr solver fails, then seeds adaptive solver with bad starting f_i
#544 opened Nov 11, 2024 by SimonBoothroyd updated Nov 11, 2024
Timeseries can be tricked by a couple bad first inputs
#283 opened Jan 22, 2018 by Lnaden updated Oct 23, 2024
15
detectEquilibration() fails if first frame is an outlier
#277 opened Nov 15, 2017 by ptmerz updated Oct 23, 2024
1
Switch from u_kln to u_kn in examples
#542 opened Sep 18, 2024 by mrshirts updated Sep 18, 2024
@mrshirts
robust method won't work with verbose=True bug
#530 opened May 15, 2024 by xiki-tempula updated Aug 5, 2024
10
Reduced Potential Definition in pymbar's FES Implementation
#534 opened Jul 9, 2024 by joaco-rgb updated Jul 9, 2024
Issue calculating FES from umbrella sampling with CV between protein C-term and N-term
#533 opened Jul 3, 2024 by Byun-jinyoung updated Jul 3, 2024
Fast way of computing the MBAR analytical error
#532 opened Jun 26, 2024 by xiki-tempula updated Jun 26, 2024
Unreasonable fes.generate_fes KeyError
#531 opened May 21, 2024 by cecilia-hong updated May 22, 2024
5
Revising the conda release strategy
#529 opened May 15, 2024 by xiki-tempula updated May 16, 2024
2
Key error due to high nbins
#528 opened Apr 19, 2024 by ashiquelal updated Apr 19, 2024
Would using pymbar's autocorrelation module be useful in reducing the number of simulations required when running non-eq FEP?
#525 opened Mar 7, 2024 by DreamCykl updated Mar 7, 2024
Should have \sum_n W_nk = 1 error with pymbar3.0.5 while analysis is working with pymbar3.0.3
#419 opened Nov 25, 2020 by hannahbaumann updated Feb 20, 2024
30
NameError: name 'ConvergenceError' is not defined
#521 opened Feb 13, 2024 by PhilippHoellmer updated Feb 13, 2024
[Q] intrinsic difficulty when solving MBAR for large number of similar thermodynamic states
#520 opened Feb 12, 2024 by svandenhaute updated Feb 12, 2024
MBAR gives a statistical error magnitudes larger than the bootstrap error.
#519 opened Jan 5, 2024 by xiki-tempula updated Jan 12, 2024
4
solver_protocol: "continuation = True" does not exhibit the desired effect? (bug vs. misunderstanding?)
#515 opened Oct 20, 2023 by denisdertli updated Oct 20, 2023
Questions on compute_expectations
#514 opened Oct 6, 2023 by gooaah updated Oct 16, 2023
2
linux-aarch64 conda support?
#474 opened Aug 22, 2022 by jmichel80 updated Oct 3, 2023
4
FES incorrectly assigns samples larger than bin bounds, also does not handle empty bins correctly
#511 opened Jun 27, 2023 by Lnaden updated Jun 27, 2023
1
Silently changing JAX default config bug pymbar 4
#496 opened Mar 31, 2023 by invemichele updated Jun 15, 2023
10
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