Skip to content

Issues: choderalab/pymbar

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

106 Open 181 Closed
106 Open 181 Closed
Author
Filter by author
Label
Filter by label
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Milestones
Filter by milestone
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Key error due to high nbins
#528 opened Apr 19, 2024 by ashiquelal
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
Shrink the overlap matrix for a subset of lambdas
#522 opened Feb 15, 2024 by xiki-tempula
NameError: name 'ConvergenceError' is not defined
#521 opened Feb 13, 2024 by PhilippHoellmer
[Q] intrinsic difficulty when solving MBAR for large number of similar thermodynamic states
#520 opened Feb 12, 2024 by svandenhaute
MBAR gives a statistical error magnitudes larger than the bootstrap error.
#519 opened Jan 5, 2024 by xiki-tempula
4
solver_protocol: "continuation = True" does not exhibit the desired effect? (bug vs. misunderstanding?)
#515 opened Oct 20, 2023 by denisdertli
Questions on compute_expectations
#514 opened Oct 6, 2023 by gooaah
2
FES incorrectly assigns samples larger than bin bounds, also does not handle empty bins correctly
#511 opened Jun 27, 2023 by Lnaden
1
pip seems to not be so happy with JAX
#501 opened Jun 5, 2023 by xiki-tempula
1
mini-batch based solver? enhancement pymbar 5
#499 opened May 14, 2023 by mrshirts
@mrshirts
Catch the issue of not being able to find ptxas bug documentation pymbar 4
#498 opened Apr 11, 2023 by xiki-tempula
1
Silently changing JAX default config bug pymbar 4
#496 opened Mar 31, 2023 by invemichele
10
MBAR uncertainty estimates in a low-overlap case
#490 opened Feb 6, 2023 by maxentile
@mrshirts
2
Check outputs.
#489 opened Jan 7, 2023 by mrshirts
jax initialization issues
#488 opened Jan 4, 2023 by mrshirts
@Lnaden
5
Examples do not work with NumPy 1.24
#484 opened Dec 20, 2022 by mattwthompson
5
The discrepancy in calculating u_kln between parallel-tempering-2dpmf.py and umbrella-sampling.py
#479 opened Nov 13, 2022 by Vinvin-Zhang
1
bin value are not unique enhancement
#477 opened Oct 30, 2022 by shawnhsueh
3
bin_edges in multi-dimension PMF can only have equal number of element in each dimension question
#476 opened Oct 30, 2022 by shawnhsueh
3
linux-aarch64 conda support?
#474 opened Aug 22, 2022 by jmichel80
4
Mapping old method argument to new API pymbar 4
#472 opened Jul 29, 2022 by mattwthompson
3
Cleanup and fixing for a 4.1 release.
#469 opened Jul 22, 2022 by mrshirts
11 tasks
Fix RTD documentation build for 3.0.7 / pymbar3-ltm pymbar-3-lts related to pymbar 3 lts support branch
#468 opened Jul 20, 2022 by mrshirts
@mrshirts
1
Examine flaky tests and see if they can be made more robust
#459 opened Jul 20, 2022 by mrshirts
ProTip! no:milestone will show everything without a milestone.