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choderalab
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perses
Experiments with expanded ensembles to explore chemical space
http://perses.readthedocs.io
MIT License
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Fix CI
#1144
mikemhenry
closed
1 year ago
2
Githubs actions CI failing
#1143
ijpulidos
closed
1 year ago
1
Remove basicConfig
#1142
dwhswenson
closed
1 year ago
5
WIP -- intuitive handling of minimization steps kwarg
#1141
ijpulidos
opened
1 year ago
1
Enable virtual bonds restraint between protein subunits by default
#1140
ijpulidos
opened
1 year ago
1
feat(docker): Add opencontainers image-spec to `Dockerfile`
#1139
SauravMaheshkar
closed
1 year ago
1
Using the faster `LangevinDynamicsMove`
#1138
ijpulidos
closed
1 year ago
2
CLI repex should use `LangevinDynamicsMove`
#1137
jchodera
closed
1 year ago
0
New CLI analysis tool
#1136
jchodera
opened
1 year ago
7
Add tool to extract equilibrium pose from simulations
#1135
JenkeScheen
opened
1 year ago
4
Ensure that perses calls `addHydrogens` on PDB files so we don't need fully protonated versions if OpenMM knows how to add the protons
#1134
jchodera
opened
1 year ago
0
Not reassigning velocities on resume for small molecule pipeline
#1133
ijpulidos
closed
1 year ago
3
Can we use espaloma-0.2.2 in perses neq calculations?
#1132
SZhang66
opened
1 year ago
0
Expose ewaldErrorTolerance argument in SystemGenerator as user parameter
#1131
jchodera
opened
1 year ago
0
can we incorporate reaction-field hybrid factory into `perses`?
#1130
dominicrufa
opened
1 year ago
6
Use `AtomMapping` objects in constraint repairs method
#1129
ijpulidos
opened
1 year ago
0
Support openff-toolkit 0.11
#1128
jchodera
closed
1 year ago
9
Update to openff 0.11 toolkit
#1127
jchodera
opened
1 year ago
0
Remove outdated devtools/conda-recipe/
#1126
jchodera
closed
1 year ago
1
Handle old constrained to new unconstrained transformation, and vice versa
#1125
ijpulidos
closed
1 year ago
1
Add openmm 8 beta to testing matrix
#1124
mikemhenry
closed
1 year ago
38
Nightly perses builds do not seem to be running
#1123
jchodera
closed
1 year ago
1
Examples run phases in expected order
#1122
ijpulidos
closed
1 year ago
4
Make examples and templates run solvent phase first
#1121
ijpulidos
closed
1 year ago
0
Change perses cli protein-ligand examples to use Tyk2
#1120
ijpulidos
closed
1 year ago
1
Nans in an unstable Non-eq. cycling calculation (across a mutation)
#1119
sukritsingh
opened
1 year ago
15
Map methyl rotors to improve efficiency
#1118
jchodera
opened
1 year ago
0
Enable only solvent phase to be specified
#1117
jchodera
opened
1 year ago
1
Investigate potential box-size dependence with new OpenMM 8 solvation algorithm
#1116
jchodera
opened
1 year ago
1
Include a CLI example where we use the geometry engine to model small transformations
#1115
jchodera
opened
1 year ago
0
Small molecule pipeline workflow is reassigning velocities by default on resume
#1114
ijpulidos
closed
1 year ago
1
test_relative_setup_charge_change failure
#1113
mikemhenry
closed
1 year ago
3
Constrained C-H bond mapped onto unconstrained C-F bond
#1112
jchodera
closed
1 year ago
13
GCMC water equilibration
#1110
jchodera
opened
2 years ago
0
Avoid using `settattr()` in lambda protocols
#1109
zhang-ivy
closed
1 year ago
3
AtomMapping distance scoring functions not working with OFF tk 0.11
#1108
richardjgowers
closed
1 year ago
3
Add analysis script variant to integrate and weight protonation/tautomer states
#1107
jchodera
closed
1 year ago
3
Add support for using Riniker reaction field electrostatics model.
#1106
jchodera
opened
2 years ago
0
Speed up RTD env generation
#1105
mikemhenry
closed
1 year ago
5
document setting ionic strengh in example
#1104
mikemhenry
closed
2 years ago
1
set aromatic draw style to `OEAromaticStyle_Circle` in atom mapper
#1103
mikemhenry
closed
1 year ago
4
fix issue with test asset name
#1102
mikemhenry
closed
2 years ago
1
make save_freq functional in validate_endstate_energies_md
#1101
mikemhenry
closed
2 years ago
1
Accept multiple ligand input files for `RelativeFEPSetup`
#1100
ijpulidos
closed
2 years ago
4
Pin to older openff-toolkit until we get openmmtools fixed
#1099
mikemhenry
closed
2 years ago
2
RESTCapableHybridTopologyFactory energy validation fails for small molecules in solvent
#1098
zhang-ivy
opened
2 years ago
2
Bug in validate_endstate_energies_md
#1097
zhang-ivy
closed
2 years ago
0
Bug in test_relative_setup_charge_change()
#1096
zhang-ivy
closed
2 years ago
2
Feat/fix ssl gpu error
#1095
mikemhenry
closed
2 years ago
4
Docs build check stopped working in github actions (GHA)
#1094
ijpulidos
closed
2 years ago
3
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