MobleyLab alchemical-analysis issues

MobleyLab / alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

MIT License

114 stars 58 forks source link

issues

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ZeroDivisionError: float division by zero

#129 gayatripanda5 closed 2 months ago
1
Migrated code from Python 2 to Python 3 for gromacs

#128 anandsahuofficial closed 4 months ago
1
setup.py installation issue

#127 sse29 closed 5 months ago
2
Inconsistent results between TI, EXP, BAR, MBAR

#126 qinghualiao opened 2 years ago
5
Overlap Matrix with MBAR issue: KeyError=2

#125 Alfa-1 opened 4 years ago
1
Compatibility with pymbar 3.0.5

#124 xiki-tempula closed 4 years ago
2
Differences between MBAR and BAR

#123 AnguseZhang closed 4 years ago
1
mbar failes with pymbar>3.0.3

#122 dnlbauer opened 4 years ago
1
O_Matrix from TI simulation of AMBER with the MBAR

#121 geraili-hosein opened 4 years ago
9
TI analysis using AMBER18

#120 DDGmichigan closed 4 years ago
5
Incompatibility with pymbar 3.0.4

#119 simonbray closed 4 years ago
2
Questions about the inconsistent results of TI, BAR and MBAR by using alchemical-analysis

#118 lpfSTX opened 5 years ago
0
GOMC parser

#117 msoroush closed 3 years ago
3
TI on AMBER18 pmemd

#116 geraili-hosein closed 5 years ago
1
import error: no module named pymbar

#115 dimitrismintis closed 5 years ago
1
ImportError: No module named pymbar

#114 dimitrismintis closed 5 years ago
0
Qestion of alchemical_analysis.py

#113 okimoto1 closed 5 years ago
3
Unable to reproduce results from Gromacs data sample

#112 chtat12 closed 5 years ago
2
Plans for librarifying alchemical-analysis functionality using alchemlyb

#111 harlor opened 5 years ago
23
Mbar result blank !

#110 JavadNoroozi closed 6 years ago
3
Use the segment indices for MBAR

#109 harlor closed 6 years ago
0
Use the total energy value and uncertainty that pymbar offers

#108 harlor closed 6 years ago
1
Update README to indicate shift towards alchemlyb

#107 davidlmobley closed 6 years ago
2
Switch to MIT

#106 davidlmobley closed 7 years ago
0
Switch to MIT license?

#105 davidlmobley closed 7 years ago
7
add few options for TI analysis and update the README file

#104 shuail closed 7 years ago
1
fix a bug in the all zeros check in the alchemical_analysis.py

#103 shuail closed 7 years ago
1
error in calculating the TI error?

#102 shuail closed 7 years ago
5
Overlap matrix issues

#101 driesvr closed 7 years ago
5
Fix bug from a line introduced/left from previous commit

#100 mrshirts closed 7 years ago
4
Some fixes to run with expanded ensembles better.

#99 mrshirts closed 7 years ago
0
Error bar estimation

#98 AlexanderWi closed 7 years ago
1
alchemical-analysis.py not computing BAR/MBAR results

#97 mqbpksi2 opened 7 years ago
40
Continuing a FEP alchemical

#96 AlexanderWi opened 7 years ago
4
Overwriting .xvg files

#95 jpthompson17 opened 7 years ago
2
Make py3 compatible

#94 davidlmobley opened 7 years ago
4
Fix for when expanded ensemble files don't have samples in all states

#93 mrshirts closed 7 years ago
1
Bug when expanded ensemble files don't have samples in all states

#92 mrshirts closed 7 years ago
1
multicore / gpu compataibility

#91 raziel81 opened 8 years ago
8
suspected memory allocation problem

#90 raziel81 closed 8 years ago
8
Auto equil

#89 matteoaldeghi opened 8 years ago
1
Automated equilibration detection

#88 matteoaldeghi opened 8 years ago
2
index 40 is out of bounds for axis 0 with size 40

#87 sanasaeed opened 8 years ago
3
Issue with Sorting input data by starting time (parser_amber.py)

#86 baribefe closed 8 years ago
8
solved issue 84 indeed

#85 FEPanalysis opened 8 years ago
3
Error in Reading GROMACS dhdl.xvg with NumPy v1.10

#84 jtp4kc closed 8 years ago
9
small ligand solvation energy calculation:error:cannot compute statistical inefficiency

#83 sanasaeed opened 8 years ago
5
Only make backups of corrupt xvgs

#82 nathanmlim closed 8 years ago
0
Corrupt xvgs check slows down gromacs parser and makes unnecessary backups

#81 nathanmlim closed 8 years ago
3
Properly merge branch to contain MBAR fixes

#80 nathanmlim closed 8 years ago
1