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MobleyLab
/
alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
MIT License
120
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60
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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
MBAR fix and workaround when cannot compute statistical inefficiency
#79
nathanmlim
closed
8 years ago
1
zero and corrupted xvg fixes
#78
nathanmlim
closed
8 years ago
3
Revert "Revert "Fix setup.py so only main executable goes in bin and put version check in setup.py""
#77
wesbarnett
closed
8 years ago
2
Fixing (#69) TI interpolation issue which arose for some cases involving zeros in lambda vectors
#76
davidlmobley
closed
8 years ago
0
Cosmetic issue with graphing TI in cases with zeros for some lambdas
#75
davidlmobley
opened
8 years ago
3
Revert "Fix setup.py so only main executable goes in bin and put version check in setup.py"
#74
davidlmobley
closed
8 years ago
0
Fix setup.py so only main executable goes in bin and put version check in setup.py
#73
wesbarnett
closed
8 years ago
8
Fix bugs related to handling of transformations without Coulomb changes and (certain) plots of free energy versus time
#72
davidlmobley
closed
8 years ago
2
Add version check for apppropriate pymbar version
#71
davidlmobley
closed
8 years ago
0
Lambda index out of bounds when accumulating free energies
#70
driesvr
closed
8 years ago
4
Problem with pymbar API; issues with cubic spline interpolation in TI
#69
driesvr
closed
8 years ago
12
[WIP] refactoring the code and some new features
#68
halx
closed
1 year ago
0
Axis limits on free energy versus time plot can be unreasonable in some cases
#67
gduarter
opened
8 years ago
2
Consider implementing extrapolation scheme for MBAR to handle AMBER's lack of endpoint data
#66
halx
closed
8 years ago
10
Generalize handling of other (non-charging/vdW) free energy components, such as for restraints, so that they don't get grouped with vdW
#65
matteoaldeghi
opened
8 years ago
4
index out of bounds error with some values of bForwrev
#64
matteoaldeghi
closed
8 years ago
5
order of methods
#63
halx
closed
8 years ago
2
The last PR was lost
#62
halx
closed
8 years ago
1
Fix for issue #52
#61
halx
closed
8 years ago
1
cannot use MBAR
#60
sanasaeed
closed
8 years ago
0
cannot use MBAR
#59
sanasaeed
closed
8 years ago
3
gromacs parser
#58
sanasaeed
closed
8 years ago
5
Uncorrelation based on those components that contribute to free energ…
#57
FEPanalysis
closed
8 years ago
1
Fixed the overlap value issue
#56
FEPanalysis
closed
8 years ago
1
Fixing issues with README files and a small issue with sire parser
#55
davidlmobley
closed
8 years ago
0
Sample SIRE data doesn't process properly
#54
davidlmobley
closed
8 years ago
3
Make overlap matrix print out leading digit when needed
#53
davidlmobley
closed
8 years ago
1
Fix AMBER parser to use units consistent with the rest of the code
#52
davidlmobley
closed
8 years ago
4
error with -c -m ti+ti-cubic
#51
halx
closed
8 years ago
4
silly bug fix
#50
halx
closed
8 years ago
0
Pymbar can't estimate bound on free energy
#49
nhoutz1
opened
8 years ago
4
General suggestions for code cleanup/improvements
#48
halx
opened
8 years ago
33
Allow parser-specific command-line options which get passed to parser to handle internally
#47
halx
closed
8 years ago
10
Add at least some form of a version tag to be printed to stdout and results.txt
#46
halx
closed
8 years ago
3
analysis TI with alchemical_analysis.py errors
#45
fglaser
closed
8 years ago
18
handle case of all zeros in all input .xvg files -- issue 14
#44
FEPanalysis
closed
8 years ago
3
Fix handling of Coulomb component and expanded ensemble data for Gromacs
#43
FEPanalysis
closed
8 years ago
1
Coulomb Free Energy
#42
bannanc
closed
8 years ago
7
desmond
#41
nathanmlim
closed
9 years ago
3
Minor cleanup to uncorrelate function
#40
nathanmlim
closed
9 years ago
2
Minor cleanups.
#39
nathanmlim
closed
9 years ago
0
Desmond Support & dE Decorrelation.
#38
nathanmlim
closed
9 years ago
0
NameError: global name 'parametersB' is not defined
#37
camizanette
closed
9 years ago
4
multiple expanded ensemble files not working
#36
mrshirts
closed
8 years ago
7
[WIP] Start of fix for analysis with multiple expanded ensemble files.
#35
mrshirts
opened
9 years ago
1
Problem with the Curve-Fitting-Method-based consistency inspector
#34
julimox
opened
9 years ago
6
MBAR method fails
#33
nividic
closed
9 years ago
3
Allow decorrelation using energy differences rather than dhdl when dhdl is not available
#32
davidlmobley
closed
9 years ago
5
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