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rinikerlab
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reeds
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
https://rinikerlab.github.io/reeds/
MIT License
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add plots for exchange frequencies per state
#97
eruijsena
closed
1 year ago
1
add plots to show the change in maxContrib state
#96
eruijsena
closed
1 year ago
1
Update the submission for multi-node with SLURM
#95
candidechamp
closed
1 year ago
0
Update plot labels
#94
chloebazin
closed
1 year ago
0
Improved OpenMM
#93
eruijsena
closed
1 year ago
0
Simplify input for optimization (rebalancing/mixed optimization)
#92
candidechamp
closed
1 year ago
1
Fix issue in occurrence sampling threshold search
#91
candidechamp
closed
1 year ago
0
Trim equilibration during analysis
#90
candidechamp
closed
1 year ago
1
New features in Hybrid Topology Maker
#89
candidechamp
closed
1 year ago
1
Added a basic calculation of free energies using M-BAR
#88
candidechamp
closed
1 year ago
0
Variable renaming and formatting changes
#87
candidechamp
closed
2 years ago
1
Simplify analysis coordinate generation
#86
candidechamp
closed
2 years ago
7
Remove two files which were never used.
#85
candidechamp
closed
2 years ago
0
Add CodeQL workflow for GitHub code scanning
#84
lgtm-com[bot]
closed
1 year ago
0
Adding input files for water reeds paper
#83
epbarros
closed
2 years ago
1
Allow single cnf input in optimization step
#82
epbarros
closed
2 years ago
0
New concat s1 only
#81
candidechamp
closed
2 years ago
0
merge slurm compatibility into improved_openmm
#80
SalomeRonja
closed
2 years ago
1
Slurm compatibility
#79
candidechamp
closed
2 years ago
2
Bug: Physical Sampling threshold detection
#78
candidechamp
closed
1 year ago
0
Add an option to only concatenate the trajectory with s = 1
#77
candidechamp
closed
2 years ago
1
Automatic search for limits
#76
candidechamp
closed
2 years ago
0
Small changes on maxContrib plots and iteration options
#75
eruijsena
closed
2 years ago
0
Set the PyGromosTools link to V1.2
#74
eruijsena
closed
2 years ago
0
RE-EDS with OpenMM
#73
SalomeRonja
closed
2 years ago
4
Add a name to SSM conformations in the title block
#72
candidechamp
closed
2 years ago
1
Add functions to automatically perform energy minimization for all end states
#71
candidechamp
closed
2 years ago
2
Add the notebook and code to generate hybrid topologies to the pipeline
#70
candidechamp
closed
1 year ago
3
Change of output location for reeds simulations analysis
#69
eruijsena
closed
2 years ago
0
link to newest pygromos1.2 commit
#68
candidechamp
closed
2 years ago
0
New replica trace plot
#67
candidechamp
closed
2 years ago
1
Rework of initialization options
#66
eruijsena
closed
2 years ago
5
Updates for protein/ligand RE-EDS + plot/bug fixes
#65
candidechamp
closed
2 years ago
7
update permittivity for amber2gromos paper
#64
SalomeRonja
closed
2 years ago
0
adding input files for benzene paper
#63
SalomeRonja
closed
2 years ago
0
Minor changes to use position restraints besides distance restraints
#62
epbarros
closed
3 years ago
0
minor improvements in dF convergence plot
#61
SalomeRonja
closed
3 years ago
0
create intermediate sopt summary plot
#60
SalomeRonja
closed
3 years ago
0
SSM approach not working on eoff rebalance branch
#59
SalomeRonja
closed
3 years ago
1
Optimization summary plot
#58
SalomeRonja
closed
3 years ago
0
number of roundtrips
#57
SalomeRonja
closed
2 years ago
5
Random Cluster Bugs
#56
RiesBen
opened
3 years ago
14
Minor rework of the submission system
#55
candidechamp
closed
3 years ago
3
added memory option to submission scripts
#54
SalomeRonja
closed
3 years ago
5
Update RE_EDS_general_analysis.py
#53
candidechamp
closed
3 years ago
0
WIP: Towards dynamic optimizations
#52
RiesBen
closed
3 years ago
1
WIP: Energy offset rebalancing
#51
RiesBen
closed
3 years ago
35
small fixes - modifications
#50
RiesBen
closed
3 years ago
6
lost files during copying from scratch
#49
SalomeRonja
closed
3 years ago
1
lower threshold for using workdir on node
#48
SalomeRonja
closed
3 years ago
5
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