choderalab pymbar issues

choderalab / pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

http://pymbar.readthedocs.io

MIT License

240 stars 93 forks source link

issues

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Should Subsampling be Recommended?

#545 fjclark opened 3 days ago
2
`hybr` solver fails, then seeds `adaptive` solver with bad starting `f_i`

#544 SimonBoothroyd opened 1 week ago
0
Including methods for equilibration detection

#543 ijpulidos opened 1 month ago
5
Switch from u_kln to u_kn in examples

#542 mrshirts opened 2 months ago
0
Issue docstring harmonic

#541 jaclark5 closed 1 month ago
6
Enthalpic and Entropic Contributions from BAR

#540 jaclark5 closed 2 months ago
14
Use self.u_kn when verbose=True in MBAR

#539 jaclark5 closed 2 months ago
5
Verbose=True with MBAR results in an error for alternative input types of u_kn

#538 jaclark5 closed 2 months ago
0
Issue gitignore

#537 jaclark5 closed 2 months ago
1
Examples output pdfs are listed in untracked files

#536 jaclark5 closed 2 months ago
3
Fix to bootstrap of free energy surfaces, affecting timing and quantitative results

#535 mrshirts opened 2 months ago
5
Reduced Potential Definition in pymbar's FES Implementation

#534 joaco-rgb opened 4 months ago
0
Issue calculating FES from umbrella sampling with CV between protein C-term and N-term

#533 Byun-jinyoung opened 4 months ago
0
Fast way of computing the MBAR analytical error

#532 xiki-tempula opened 4 months ago
0
Unreasonable fes.generate_fes KeyError

#531 cecilia-hong opened 6 months ago
5
robust method won't work with verbose=True

#530 xiki-tempula opened 6 months ago
10
Revising the conda release strategy

#529 xiki-tempula opened 6 months ago
2
Key error due to high nbins

#528 ashiquelal opened 7 months ago
0
fix minor typos

#527 schuhmc closed 7 months ago
0
Update to Python 3.12

#526 Lnaden closed 8 months ago
2
Would using pymbar's autocorrelation module be useful in reducing the number of simulations required when running non-eq FEP?

#525 DreamCykl opened 8 months ago
0
Support newer jax version (0.4.25) where jax.config.config is removed.

#524 nielskm closed 8 months ago
1
BAR estimate without overlap

#523 wiederm closed 8 months ago
2
Shrink the overlap matrix for a subset of lambdas

#522 xiki-tempula closed 6 months ago
0
NameError: name 'ConvergenceError' is not defined

#521 PhilippHoellmer opened 9 months ago
0
[Q] intrinsic difficulty when solving MBAR for large number of similar thermodynamic states

#520 svandenhaute opened 9 months ago
0
MBAR gives a statistical error magnitudes larger than the bootstrap error.

#519 xiki-tempula opened 10 months ago
4
Assorted maintenance updates

#517 mattwthompson opened 1 year ago
2
Support Python 3.12

#516 mattwthompson closed 8 months ago
1
solver_protocol: "continuation = True" does not exhibit the desired effect? (bug vs. misunderstanding?)

#515 denisdertli opened 1 year ago
0
Questions on `compute_expectations`

#514 gooaah opened 1 year ago
2
Fixed example bug and updated output.

#513 mrshirts closed 1 year ago
4
Fix a small bug in the timeseries test, test against min and max versions

#512 Lnaden closed 1 year ago
1
FES incorrectly assigns samples larger than bin bounds, also does not handle empty bins correctly

#511 Lnaden opened 1 year ago
1
fixes RTD build

#510 mikemhenry closed 1 year ago
1
Make using JAX (or any accelerator) an Instanced Python class (and toggle)

#509 Lnaden opened 1 year ago
4
Make using JAX (or any accelerator) a toggle

#508 Lnaden closed 1 year ago
7
Correct docstring default value

#507 badisa closed 1 year ago
1
Wrap the preconditioned jit

#506 Lnaden closed 1 year ago
1
Correctly stagger JIT until first call

#505 Lnaden closed 1 year ago
1
Warn about JAX bitsize changes

#504 Lnaden closed 1 year ago
1
Make JAX an optional dependency

#503 Lnaden closed 1 year ago
2
[DNM] Update fes.py (BUG!)

#502 rosadche closed 1 year ago
4
pip seems to not be so happy with JAX

#501 xiki-tempula opened 1 year ago
1
Optional JAX dependency

#500 Lnaden closed 1 year ago
30
mini-batch based solver?

#499 mrshirts opened 1 year ago
0
Catch the issue of not being able to find ptxas

#498 xiki-tempula opened 1 year ago
1
see if tests pass without 64 bit floats

#497 mikemhenry opened 1 year ago
1
Silently changing JAX default config

#496 invemichele opened 1 year ago
10
use mamba to build docs on the lts branch

#495 mikemhenry closed 1 year ago
2