Issues

• Inconsistent results between TI, EXP, BAR, MBAR

  MobleyLab/alchemical-analysis#126 · Filter by author qinghualiao opened on Oct 20, 2021
  5

• Overlap Matrix with MBAR issue: KeyError=2

  MobleyLab/alchemical-analysis#125 · Filter by author Alfa-1 opened on Sep 15, 2020
  1

• O_Matrix from TI simulation of AMBER with the MBAR

  MobleyLab/alchemical-analysis#121 · Filter by author geraili-hosein opened on Feb 21, 2020
  9

• Questions about the inconsistent results of TI, BAR and MBAR by using alchemical-analysis

  MobleyLab/alchemical-analysis#118 · Filter by author lpfSTX opened on Jul 9, 2019

• Plans for librarifying alchemical-analysis functionality using alchemlyb

  MobleyLab/alchemical-analysis#111 · Filter by author harlor opened on Oct 19, 2018
  23

• alchemical-analysis.py not computing BAR/MBAR results

  MobleyLab/alchemical-analysis#97 · Filter by author mqbpksi2 opened on Jan 26, 2017
  40

• Continuing a FEP alchemical

  enhancementhelp wanted
  MobleyLab/alchemical-analysis#96 · Filter by author AlexanderWi opened on Jan 23, 2017
  4

• Overwriting .xvg files

  MobleyLab/alchemical-analysis#95 · Filter by author jpthompson17 opened on Jan 16, 2017
  2

• Make py3 compatible

  MobleyLab/alchemical-analysis#94 · Filter by author davidlmobley opened on Jan 12, 2017
  4

• multicore / gpu compataibility

  MobleyLab/alchemical-analysis#91 · Filter by author raziel81 opened on Aug 25, 2016
  8

• Automated equilibration detection

  MobleyLab/alchemical-analysis#88 · Filter by author matteoaldeghi opened on Apr 28, 2016
  2

• index 40 is out of bounds for axis 0 with size 40

  MobleyLab/alchemical-analysis#87 · Filter by author sanasaeed opened on Apr 25, 2016
  3

• small ligand solvation energy calculation:error:cannot compute statistical inefficiency

  MobleyLab/alchemical-analysis#83 · Filter by author sanasaeed opened on Mar 10, 2016
  5

• Cosmetic issue with graphing TI in cases with zeros for some lambdas

  Long term
  MobleyLab/alchemical-analysis#75 · Filter by author davidlmobley opened on Feb 9, 2016
  3

• Axis limits on free energy versus time plot can be unreasonable in some cases

  MobleyLab/alchemical-analysis#67 · Filter by author gduarter opened on Jan 13, 2016
  2

• Generalize handling of other (non-charging/vdW) free energy components, such as for restraints, so that they don't get grouped with vdW

  enhancement
  MobleyLab/alchemical-analysis#65 · Filter by author matteoaldeghi opened on Jan 13, 2016
  4

• Pymbar can't estimate bound on free energy

  High priority
  MobleyLab/alchemical-analysis#49 · Filter by author nhoutz1 opened on Dec 16, 2015
  4

• General suggestions for code cleanup/improvements

  question
  MobleyLab/alchemical-analysis#48 · Filter by author halx opened on Dec 13, 2015
  33

• Problem with the Curve-Fitting-Method-based consistency inspector

  High priority
  MobleyLab/alchemical-analysis#34 · Filter by author julimox opened on Oct 22, 2015
  6

  

• Make python3 compatible

  Long term
  MobleyLab/alchemical-analysis#21 · Filter by author davidlmobley opened on May 26, 2015

• Make an official (numbered) release version of the code published with our paper, then begin following version numbering conventions

  MobleyLab/alchemical-analysis#13 · Filter by author davidlmobley opened on Apr 28, 2015
  1

  

• Make plain-text output (results.txt) have appropriate significant figures

  enhancement
  MobleyLab/alchemical-analysis#8 · Filter by author davidlmobley opened on Apr 23, 2015

• Make it auto-install dependencies (pymbar, etc)

  enhancementhelp wanted
  MobleyLab/alchemical-analysis#7 · Filter by author davidlmobley opened on Apr 23, 2015
  3

• Long-term: Implement automated testing of alchemical-analysis

  enhancement
  MobleyLab/alchemical-analysis#5 · Filter by author davidlmobley opened on Apr 23, 2015