Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / MobleyLab/alchemical-analysis issues and pull requests

#126 - Inconsistent results between TI, EXP, BAR, MBAR

Issue - State: open - Opened by qinghualiao over 3 years ago - 5 comments

#125 - Overlap Matrix with MBAR issue: KeyError=2

Issue - State: open - Opened by Alfa-1 over 4 years ago - 1 comment

#124 - Compatibility with pymbar 3.0.5

Issue - State: closed - Opened by xiki-tempula over 4 years ago - 2 comments

#123 - Differences between MBAR and BAR

Issue - State: closed - Opened by AnguseZhang almost 5 years ago - 1 comment

#122 - mbar failes with pymbar>3.0.3

Pull Request - State: open - Opened by dnlbauer almost 5 years ago - 1 comment

#121 - O_Matrix from TI simulation of AMBER with the MBAR

Issue - State: open - Opened by geraili-hosein almost 5 years ago - 9 comments

#120 - TI analysis using AMBER18

Issue - State: closed - Opened by DDGmichigan almost 5 years ago - 5 comments

#119 - Incompatibility with pymbar 3.0.4

Issue - State: closed - Opened by simonbray about 5 years ago - 2 comments

#117 - GOMC parser

Issue - State: closed - Opened by msoroush almost 6 years ago - 3 comments

#116 - TI on AMBER18 pmemd

Issue - State: closed - Opened by geraili-hosein almost 6 years ago - 1 comment

#115 - import error: no module named pymbar

Issue - State: closed - Opened by dimitrismintis about 6 years ago - 1 comment

#114 - ImportError: No module named pymbar

Issue - State: closed - Opened by dimitrismintis about 6 years ago

#113 - Qestion of alchemical_analysis.py

Issue - State: closed - Opened by okimoto1 about 6 years ago - 3 comments

#112 - Unable to reproduce results from Gromacs data sample

Issue - State: closed - Opened by chtat12 over 6 years ago - 2 comments

#111 - Plans for librarifying alchemical-analysis functionality using alchemlyb

Issue - State: open - Opened by harlor over 6 years ago - 23 comments

#110 - Mbar result blank !

Issue - State: closed - Opened by JavadNoroozi over 6 years ago - 3 comments

#109 - Use the segment indices for MBAR

Pull Request - State: closed - Opened by harlor over 6 years ago

#108 - Use the total energy value and uncertainty that pymbar offers

Pull Request - State: closed - Opened by harlor almost 7 years ago - 1 comment

#107 - Update README to indicate shift towards alchemlyb

Pull Request - State: closed - Opened by davidlmobley about 7 years ago - 2 comments

#106 - Switch to MIT

Pull Request - State: closed - Opened by davidlmobley over 7 years ago

#105 - Switch to MIT license?

Issue - State: closed - Opened by davidlmobley over 7 years ago - 7 comments

#104 - add few options for TI analysis and update the README file

Pull Request - State: closed - Opened by shuail over 7 years ago - 1 comment

#103 - fix a bug in the all zeros check in the alchemical_analysis.py

Pull Request - State: closed - Opened by shuail over 7 years ago - 1 comment

#102 - error in calculating the TI error?

Issue - State: closed - Opened by shuail over 7 years ago - 5 comments

#101 - Overlap matrix issues

Issue - State: closed - Opened by driesvr almost 8 years ago - 5 comments

#100 - Fix bug from a line introduced/left from previous commit

Pull Request - State: closed - Opened by mrshirts almost 8 years ago - 4 comments

#99 - Some fixes to run with expanded ensembles better.

Pull Request - State: closed - Opened by mrshirts almost 8 years ago

#98 - Error bar estimation

Issue - State: closed - Opened by AlexanderWi almost 8 years ago - 1 comment

#97 - alchemical-analysis.py not computing BAR/MBAR results

Issue - State: open - Opened by mqbpksi2 about 8 years ago - 40 comments

#96 - Continuing a FEP alchemical

Issue - State: open - Opened by AlexanderWi about 8 years ago - 4 comments
Labels: enhancement, help wanted

#95 - Overwriting .xvg files

Issue - State: open - Opened by jpthompson17 about 8 years ago - 2 comments

#94 - Make py3 compatible

Issue - State: open - Opened by davidlmobley about 8 years ago - 4 comments

#93 - Fix for when expanded ensemble files don't have samples in all states

Pull Request - State: closed - Opened by mrshirts over 8 years ago - 1 comment

#92 - Bug when expanded ensemble files don't have samples in all states

Issue - State: closed - Opened by mrshirts over 8 years ago - 1 comment

#91 - multicore / gpu compataibility

Issue - State: open - Opened by raziel81 over 8 years ago - 8 comments

#90 - suspected memory allocation problem

Issue - State: closed - Opened by raziel81 over 8 years ago - 8 comments

#89 - Auto equil

Pull Request - State: open - Opened by matteoaldeghi almost 9 years ago - 1 comment

#88 - Automated equilibration detection

Issue - State: open - Opened by matteoaldeghi almost 9 years ago - 2 comments

#87 - index 40 is out of bounds for axis 0 with size 40

Issue - State: open - Opened by sanasaeed almost 9 years ago - 3 comments

#86 - Issue with Sorting input data by starting time (parser_amber.py)

Issue - State: closed - Opened by baribefe almost 9 years ago - 8 comments

#85 - solved issue 84 indeed

Pull Request - State: open - Opened by FEPanalysis almost 9 years ago - 3 comments

#84 - Error in Reading GROMACS dhdl.xvg with NumPy v1.10

Issue - State: closed - Opened by jtp4kc almost 9 years ago - 9 comments

#82 - Only make backups of corrupt xvgs

Pull Request - State: closed - Opened by nathanmlim almost 9 years ago

#81 - Corrupt xvgs check slows down gromacs parser and makes unnecessary backups

Issue - State: closed - Opened by nathanmlim almost 9 years ago - 3 comments
Labels: enhancement, Medium priority

#80 - Properly merge branch to contain MBAR fixes

Pull Request - State: closed - Opened by nathanmlim almost 9 years ago - 1 comment

#79 - MBAR fix and workaround when cannot compute statistical inefficiency

Pull Request - State: closed - Opened by nathanmlim almost 9 years ago - 1 comment

#78 - zero and corrupted xvg fixes

Pull Request - State: closed - Opened by nathanmlim almost 9 years ago - 3 comments

#75 - Cosmetic issue with graphing TI in cases with zeros for some lambdas

Issue - State: open - Opened by davidlmobley almost 9 years ago - 3 comments
Labels: Long term

#73 - Fix setup.py so only main executable goes in bin and put version check in setup.py

Pull Request - State: closed - Opened by wesbarnett almost 9 years ago - 8 comments

#71 - Add version check for apppropriate pymbar version

Pull Request - State: closed - Opened by davidlmobley almost 9 years ago

#70 - Lambda index out of bounds when accumulating free energies

Issue - State: closed - Opened by driesvr about 9 years ago - 4 comments

#69 - Problem with pymbar API; issues with cubic spline interpolation in TI

Issue - State: closed - Opened by driesvr about 9 years ago - 12 comments

#68 - [WIP] refactoring the code and some new features

Pull Request - State: closed - Opened by halx about 9 years ago

#67 - Axis limits on free energy versus time plot can be unreasonable in some cases

Issue - State: open - Opened by gduarter about 9 years ago - 2 comments

#66 - Consider implementing extrapolation scheme for MBAR to handle AMBER's lack of endpoint data

Issue - State: closed - Opened by halx about 9 years ago - 10 comments
Labels: enhancement, Medium priority

#64 - index out of bounds error with some values of bForwrev

Issue - State: closed - Opened by matteoaldeghi about 9 years ago - 5 comments

#63 - order of methods

Issue - State: closed - Opened by halx about 9 years ago - 2 comments

#62 - The last PR was lost

Pull Request - State: closed - Opened by halx about 9 years ago - 1 comment

#61 - Fix for issue #52

Pull Request - State: closed - Opened by halx about 9 years ago - 1 comment

#60 - cannot use MBAR

Issue - State: closed - Opened by sanasaeed about 9 years ago

#59 - cannot use MBAR

Issue - State: closed - Opened by sanasaeed about 9 years ago - 3 comments

#58 - gromacs parser

Issue - State: closed - Opened by sanasaeed about 9 years ago - 5 comments

#57 - Uncorrelation based on those components that contribute to free energ…

Pull Request - State: closed - Opened by FEPanalysis about 9 years ago - 1 comment

#56 - Fixed the overlap value issue

Pull Request - State: closed - Opened by FEPanalysis about 9 years ago - 1 comment

#55 - Fixing issues with README files and a small issue with sire parser

Pull Request - State: closed - Opened by davidlmobley about 9 years ago

#54 - Sample SIRE data doesn't process properly

Issue - State: closed - Opened by davidlmobley about 9 years ago - 3 comments

#53 - Make overlap matrix print out leading digit when needed

Issue - State: closed - Opened by davidlmobley about 9 years ago - 1 comment
Labels: bug, High priority

#52 - Fix AMBER parser to use units consistent with the rest of the code

Issue - State: closed - Opened by davidlmobley about 9 years ago - 4 comments

#51 - error with -c -m ti+ti-cubic

Issue - State: closed - Opened by halx about 9 years ago - 4 comments
Labels: enhancement, Medium priority

#50 - silly bug fix

Pull Request - State: closed - Opened by halx about 9 years ago

#49 - Pymbar can't estimate bound on free energy

Issue - State: open - Opened by nhoutz1 about 9 years ago - 4 comments
Labels: High priority

#48 - General suggestions for code cleanup/improvements

Issue - State: open - Opened by halx about 9 years ago - 33 comments
Labels: question

#47 - Allow parser-specific command-line options which get passed to parser to handle internally

Issue - State: closed - Opened by halx about 9 years ago - 10 comments
Labels: enhancement, Long term

#46 - Add at least some form of a version tag to be printed to stdout and results.txt

Issue - State: closed - Opened by halx about 9 years ago - 3 comments
Labels: High priority

#45 - analysis TI with alchemical_analysis.py errors

Issue - State: closed - Opened by fglaser about 9 years ago - 18 comments

#44 - handle case of all zeros in all input .xvg files -- issue 14

Pull Request - State: closed - Opened by FEPanalysis about 9 years ago - 3 comments

#43 - Fix handling of Coulomb component and expanded ensemble data for Gromacs

Pull Request - State: closed - Opened by FEPanalysis about 9 years ago - 1 comment

#42 - Coulomb Free Energy

Issue - State: closed - Opened by bannanc about 9 years ago - 7 comments

#36 - multiple expanded ensemble files not working

Issue - State: closed - Opened by mrshirts over 9 years ago - 7 comments

#35 - [WIP] Start of fix for analysis with multiple expanded ensemble files.

Pull Request - State: open - Opened by mrshirts over 9 years ago - 1 comment

#34 - Problem with the Curve-Fitting-Method-based consistency inspector

Issue - State: open - Opened by julimox over 9 years ago - 6 comments
Labels: High priority

#32 - Allow decorrelation using energy differences rather than dhdl when dhdl is not available

Pull Request - State: closed - Opened by davidlmobley over 9 years ago - 5 comments

#31 - New parser

Pull Request - State: closed - Opened by halx over 9 years ago - 5 comments

#30 - Change README.md to properly point

Issue - State: closed - Opened by mrshirts over 9 years ago - 3 comments

#28 - Documentation clarification for u_klt matrix

Issue - State: closed - Opened by nathanmlim over 9 years ago
Labels: question

#27 - Inaccurate decorrelation times when lambda_coul and lambda_vdw change at different times.

Issue - State: closed - Opened by mrshirts over 9 years ago - 11 comments
Labels: High priority

#26 - -a amber -m all throws error

Issue - State: closed - Opened by foxth over 9 years ago - 9 comments

#21 - Make python3 compatible

Issue - State: open - Opened by davidlmobley over 9 years ago
Labels: Long term

#15 - Provide a utility tool to attempt cleanup of bad GROMACS data

Issue - State: closed - Opened by davidlmobley over 9 years ago - 3 comments
Labels: enhancement

#14 - Properly handle case of all zeros in all input .xvg files

Issue - State: closed - Opened by davidlmobley over 9 years ago - 1 comment
Labels: High priority

#7 - Make it auto-install dependencies (pymbar, etc)

Issue - State: open - Opened by davidlmobley almost 10 years ago - 3 comments
Labels: enhancement, help wanted

#6 - Make conda installable

Issue - State: closed - Opened by davidlmobley almost 10 years ago - 2 comments
Labels: enhancement, help wanted