MobleyLab/alchemical-analysis

Issues

• TypeError: iter() returned non-iterator of type 'SectionParser'

  #131 opened 2 months ago by Qli97
  0

• Free energy difference as a function of time

  #130 opened 3 months ago by pallavsen007
  1

• ZeroDivisionError: float division by zero

  #129 opened 5 months ago by gayatripanda5
  1

• setup.py installation issue

  #127 opened 9 months ago by sse29
  2

• Inconsistent results between TI, EXP, BAR, MBAR

  #126 opened 3 years ago by qinghualiao
  5

• O_Matrix from TI simulation of AMBER with the MBAR

  #121 opened 5 years ago by geraili-hosein
  9

• GOMC parser

  #117 opened 4 years ago by msoroush
  3

• Overlap Matrix with MBAR issue: KeyError=2

  #125 opened 4 years ago by Alfa-1
  1

• Compatibility with pymbar 3.0.5

  #124 opened 4 years ago by xiki-tempula
  2

• Differences between MBAR and BAR

  #123 opened 5 years ago by AnguseZhang
  1

• TI analysis using AMBER18

  #120 opened 5 years ago by DDGmichigan
  5

• Incompatibility with pymbar 3.0.4

  #119 opened 5 years ago by simonbray
  2

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

  #118 opened 6 years ago by lpfSTX
  0

• TI on AMBER18 pmemd

  #116 opened 6 years ago by geraili-hosein
  1

• Qestion of alchemical_analysis.py

  #113 opened 6 years ago by okimoto1
  3

• import error: no module named pymbar

  #115 opened 6 years ago by dimitrismintis
  1

• ImportError: No module named pymbar

  #114 opened 6 years ago by dimitrismintis
  0

• Plans for librarifying alchemical-analysis functionality using alchemlyb

  #111 opened 6 years ago by harlor
  23

• Unable to reproduce results from Gromacs data sample

  #112 opened 6 years ago by chtat12
  2

• Mbar result blank !

  #110 opened 6 years ago by JavadNoroozi
  3

• Switch to MIT license?

  #105 opened 7 years ago by davidlmobley
  7

• error in calculating the TI error?

  #102 opened 7 years ago by shuail
  5

• Error bar estimation

  #98 opened 7 years ago by AlexanderWi
  1

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

  #97 opened 8 years ago by mqbpksi2
  40

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

  #75 opened 9 years ago by davidlmobley
  3

• Overlap matrix issues

  #101 opened 8 years ago by driesvr
  5

• Continuing a FEP alchemical

  #96 opened 8 years ago by AlexanderWi
  4

• Overwriting .xvg files

  #95 opened 8 years ago by jpthompson17
  2

• Make py3 compatible

  #94 opened 8 years ago by davidlmobley
  4

• Bug when expanded ensemble files don't have samples in all states

  #92 opened 8 years ago by mrshirts
  1

• Error in Reading GROMACS dhdl.xvg with NumPy v1.10

  #84 opened 8 years ago by jtp4kc
  9

• Issue with Sorting input data by starting time (parser_amber.py)

  #86 opened 8 years ago by baribefe
  8

• multicore / gpu compataibility

  #91 opened 8 years ago by raziel81
  8

• suspected memory allocation problem

  #90 opened 8 years ago by raziel81
  8

• Consider implementing extrapolation scheme for MBAR to handle AMBER's lack of endpoint data

  #66 opened 9 years ago by halx
  10

• Automated equilibration detection

  #88 opened 9 years ago by matteoaldeghi
  2

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

  #87 opened 9 years ago by sanasaeed
  3

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

  #83 opened 9 years ago by sanasaeed
  5

• Corrupt xvgs check slows down gromacs parser and makes unnecessary backups

  #81 opened 9 years ago by nathanmlim
  3

• Problem with pymbar API; issues with cubic spline interpolation in TI

  #69 opened 9 years ago by driesvr
  12

• index out of bounds error with some values of bForwrev

  #64 opened 9 years ago by matteoaldeghi
  5

• Lambda index out of bounds when accumulating free energies

  #70 opened 9 years ago by driesvr
  4

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

  #65 opened 9 years ago by matteoaldeghi
  4

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

  #67 opened 9 years ago by gduarter
  2

• gromacs parser

  #58 opened 9 years ago by sanasaeed
  5

• order of methods

  #63 opened 9 years ago by halx
  2

• cannot use MBAR

  #59 opened 9 years ago by sanasaeed
  3

• Sample SIRE data doesn't process properly

  #54 opened 9 years ago by davidlmobley
  3

• cannot use MBAR

  #60 opened 9 years ago by sanasaeed
  0

• Make overlap matrix print out leading digit when needed

  #53 opened 9 years ago by davidlmobley
  1