choderalab / pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

http://pymbar.readthedocs.io

choderalab/pymbar Issues

Issue calculating FES from umbrella sampling with CV between protein C-term and N-term
Updated 16 days ago
Fast way of computing the MBAR analytical error
Updated 22 days ago
Unreasonable fes.generate_fes KeyError
Updated 2 months ago5
Revising the conda release strategy
Updated 2 months ago2
robust method won't work with verbose=True
Updated 2 months ago3
Shrink the overlap matrix for a subset of lambdas
Closed 2 months ago
Key error due to high nbins
Updated 3 months ago
BAR estimate without overlap
Closed 4 months ago2
Would using pymbar's autocorrelation module be useful in reducing the number of simulations required when running non-eq FEP?
Updated 4 months ago
NameError: name 'ConvergenceError' is not defined
Updated 5 months ago
[Q] intrinsic difficulty when solving MBAR for large number of similar thermodynamic states
Updated 5 months ago
MBAR gives a statistical error magnitudes larger than the bootstrap error.
Updated 6 months ago4
solver_protocol: "continuation = True" does not exhibit the desired effect? (bug vs. misunderstanding?)
Updated 9 months ago
Questions on `compute_expectations`
Updated 9 months ago2
linux-aarch64 conda support?
Updated 10 months ago4
Optional JAX dependency
Closed a year ago30
FES incorrectly assigns samples larger than bin bounds, also does not handle empty bins correctly
Updated a year ago1
Silently changing JAX default config
Updated a year ago10
pip seems to not be so happy with JAX
Updated a year ago1
mini-batch based solver?
Updated a year ago
Catch the issue of not being able to find ptxas
Updated a year ago1
readthdocs not building; looks like config issue
Closed a year ago4
MBAR uncertainty estimates in a low-overlap case
Updated a year ago2
Check outputs.
Updated 2 years ago
jax initialization issues
Updated 2 years ago5
Examples do not work with NumPy 1.24
Updated 2 years ago5
Problem with parallel-tempering-2dpmf.py
Closed 2 years ago1
The discrepancy in calculating u_kln between parallel-tempering-2dpmf.py and umbrella-sampling.py
Updated 2 years ago1
bin_edges in multi-dimension PMF can only have equal number of element in each dimension
Updated 2 years ago3
bin value are not unique
Updated 2 years ago3
pymbar 3.1 release not available through PyPI
Closed 2 years ago1
Mapping old `method` argument to new API
Updated 2 years ago3
Fix RTD documentation build for 3.0.7 / pymbar3-ltm
Updated 2 years ago1
Cleanup and fixing for a 4.1 release.
Updated 2 years ago
Examine flaky tests and see if they can be made more robust
Updated 2 years ago
Decide on what "robust" and "default" solvers are for pymbar before 4.0 launch.
Updated 2 years ago
what's the feature of a bad weights matrix?
Updated 2 years ago1
Detailed 4.0 project planning for release
Updated 2 years ago8
Update documentation for readthedocs (Levi does any autoconfiguration, MRS adds necessary text).
Closed 2 years ago
pymbar and high or low potential energy values
Closed 2 years ago2
MBAR estimator automatically choosing the usable method
Updated 2 years ago4
Add tests for BAR methods
Closed 2 years ago
Small README fix - no import of MBAR
Updated 2 years ago3
Add methods to compute overlap and effective sample sizes for BAR?
Closed 2 years ago4
Verify BAR is working with constant energy states
Updated 2 years ago
nan uncertainty estimates
Updated 2 years ago10
Build for Python for 3.9?
Closed 3 years ago4
How to get the u_kn matrix by reduced potential energy?
Closed 3 years ago
Remove corrupted lines in xvg files
Closed 3 years ago2
Docs seem to be out of date
Updated 3 years ago