wehs7661 ensemble_md issues

wehs7661 / ensemble_md

A python package for performing GROMACS simulation ensembles

MIT License

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Conda release of ensemble_md

#63 wehs7661 opened 3 days ago
0
A checklist for version 1.1.0 of ensemble_md

#62 wehs7661 opened 3 days ago
0
Adding contribution guidelines

#61 wehs7661 closed 3 days ago
1
Simplify and tweak the functionalities for MT-REXEE

#60 wehs7661 opened 4 days ago
0
Unit tests for MT-REXEE functionalities

#59 wehs7661 opened 4 days ago
1
MT-REXEE development

#58 wehs7661 opened 5 days ago
1
Mtrexee dev

#57 ajfriedman22 opened 5 days ago
0
Mtrexee dev

#56 ajfriedman22 closed 5 days ago
0
An overview of CircleCI issues

#55 wehs7661 opened 1 month ago
2
Final tweaks before releasing version 1.0.0

#54 wehs7661 closed 1 month ago
2
Enable a CircleCI build based on Python 3.12

#53 wehs7661 closed 1 month ago
1
Add tutorials of running and analyzing REXEE simulations

#52 wehs7661 closed 1 month ago
1
Update the documentation of `ensemble_md`

#51 wehs7661 closed 4 months ago
1
A list of non-urgent but important enhancements for future consideration

#50 wehs7661 opened 4 months ago
0
Further refine the unit tests of `ensemble_md`

#49 wehs7661 closed 4 months ago
2
Refine the docstrings for all modules in `ensemble_md`.

#48 wehs7661 closed 4 months ago
0
Refactor some utility functions

#47 wehs7661 closed 5 months ago
1
Improve the documentation of `ensemble_md`

#46 wehs7661 closed 4 months ago
3
Information about the simulation is not printed on-the-fly to `run_REXEE_log.txt`

#45 wehs7661 opened 5 months ago
0
Modify `config.yaml` of CircleCI to allow rerunning failed tests

#44 wehs7661 closed 1 month ago
1
A checklist for docstring proofreading

#43 wehs7661 closed 4 months ago
1
Adding more unit tests for the package

#42 wehs7661 closed 5 months ago
1
A list of todos for the next release of `ensemble_md`

#41 wehs7661 closed 4 months ago
1
Adding unit tests for functions that use MPI

#40 wehs7661 closed 5 months ago
1
Add relevant functionalities for estimating the spectral gap uncertainties

#39 wehs7661 closed 5 months ago
0
Adding example simulation inputs used in the REXEE paper

#38 wehs7661 closed 5 months ago
1
Add unit tests for `replica_exchange_EE.py`, the `utils` module and a part of the `analysis` module

#37 wehs7661 closed 5 months ago
1
Some minor tweaks for the analysis codes

#36 wehs7661 closed 6 months ago
1
Adapt the data to be pickled for cases with `subsampling_avg = True`

#35 wehs7661 closed 6 months ago
1
Enable extension/continuation of weight-updating REXEE simulations

#34 wehs7661 opened 6 months ago
0
Update the theory section in the documentation

#33 wehs7661 closed 5 months ago
1
Remove the YAML parameter `acceptance`

#32 wehs7661 closed 10 months ago
1
Refactor weight combination schemes

#31 wehs7661 closed 10 months ago
1
Refactor weight combination schemes

#30 wehs7661 closed 10 months ago
1
Functionalities for testing purposes or of less usage should be deprecated

#29 wehs7661 closed 10 months ago
1
Fix the calculation of acceptance ratio in REXEE simulations

#28 wehs7661 closed 10 months ago
1
Rename the EEXE method as REXEE method

#27 wehs7661 closed 10 months ago
1
Refine the documentation of the package

#26 wehs7661 closed 5 months ago
1
Implement the method for histogram correction

#25 wehs7661 closed 10 months ago
1
Refactoring codes for weight combination

#24 wehs7661 closed 1 year ago
1
Resolve the issue of poor sampling

#23 wehs7661 closed 1 year ago
5
Fix the issue of poor sampling in the alchemical space

#22 wehs7661 closed 1 year ago
2
Fixed the bugs relevant to coordinate modification

#21 wehs7661 closed 1 year ago
5
Add the CLI `run_EEXE_mpi`

#20 wehs7661 opened 1 year ago
0
Enabled specifying different simulation inputs/parameters for different replicas

#19 wehs7661 closed 1 year ago
1
Enable different simulation input files for different replicas

#18 wehs7661 closed 1 year ago
1
Fixed-weight EEXE simulations should have the choice to be initiated by different sets of weights for different replicas

#17 wehs7661 closed 1 year ago
2
Extend EEXE Framework to allow coordinate manipulation

#16 wehs7661 closed 1 year ago
1
Enable coordinate modification in the EEXE framework

#15 wehs7661 closed 1 year ago
4
Reducing the overhead in parallelizing simulations

#14 wehs7661 closed 1 year ago
1