issues
search
choderalab
/
perses
Experiments with expanded ensembles to explore chemical space
http://perses.readthedocs.io
MIT License
181
stars
51
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
OpenEye dependencies are a barrier to using perses
#1248
danielguion
opened
5 days ago
1
IndexError with `_vacdg_history` if there is no vacuum trajectory
#1247
slochower
opened
7 months ago
3
Improved reporting and state detection when passing tautomers as `old_residue`
#1246
sukritsingh
opened
7 months ago
0
Retrieving exact topology used for an endpoint in a relative transformation
#1245
slochower
closed
7 months ago
11
Update README?
#1244
zhang-ivy
opened
11 months ago
1
[DNM] Test/openmm 8.1.0rc1
#1243
mikemhenry
closed
11 months ago
10
[DNM] Test openmm 8.1 release candidate
#1242
ijpulidos
closed
1 year ago
3
Allow specification of mapping dictionary in the pipeline
#1241
ijpulidos
opened
1 year ago
0
[DNM] test openmm 8.1
#1240
mikemhenry
closed
1 year ago
2
Fix incorrect implementation of logsumexp
#1239
mikemhenry
closed
1 year ago
1
Fix incorrect implementation of logsumexp
#1238
badisa
closed
1 year ago
6
Test new open ffmast fix
#1237
mikemhenry
opened
1 year ago
6
Change log for 0.10.3 release
#1236
mikemhenry
closed
1 year ago
2
0.10.x merge into main
#1235
mikemhenry
closed
1 year ago
6
Fix spectator support
#1233
ijpulidos
closed
1 year ago
6
Error with spectator ligands
#1232
arjun-nufc
closed
9 months ago
8
Support for use of custom force fields (e.g., one generated from openff-bespokefit)
#1231
arjun-nufc
closed
9 months ago
5
Fix/issue 1194
#1230
mikemhenry
closed
1 year ago
7
Fix/issue 1196
#1229
mikemhenry
closed
1 year ago
1
MPI example with dipeptide mutation
#1228
ijpulidos
closed
1 year ago
1
Realtime analysis interval to default to checkpoint interval
#1227
ijpulidos
closed
1 year ago
2
Allow user to specify list of atom indices to override default behavior for selecting the REST region
#1226
zhang-ivy
opened
1 year ago
0
Fix potential bug in counterion implementation: get_water_indices()
#1225
zhang-ivy
opened
1 year ago
0
Adapt MPi example with perses at least for protein mutation
#1224
ijpulidos
closed
1 year ago
1
Clean examples -- CLI protein-ligand example for Tyk2
#1223
ijpulidos
closed
1 year ago
1
Protein mutation protocol for alchemiscale
#1222
ijpulidos
opened
1 year ago
1
Migrate from PDB to PDBx/mmcif
#1221
ijpulidos
opened
1 year ago
1
Make `offline-freq` be the same as `checkpoint_interval` by default
#1220
jthorton
closed
1 year ago
1
Duplicate instances of `self._setup_complex_phase()` in relative_setup.py
#1219
zhang-ivy
opened
1 year ago
2
CI minor fixes. Allow codecov to fail.
#1218
mikemhenry
closed
1 year ago
0
CI miscellaneous fixes
#1217
ijpulidos
closed
1 year ago
1
perses with mpi
#1216
mikemhenry
opened
1 year ago
1
[Draft] Self-consistently parameterize protein-ligand with espaloma-0.3.0
#1215
kntkb
opened
1 year ago
1
Remove example testing
#1214
mikemhenry
closed
1 year ago
1
Make sure we merge latest 0.10 branch before working on 0.11 refactor
#1213
ijpulidos
opened
1 year ago
0
run CI on new 0.10.x branch
#1212
mikemhenry
closed
1 year ago
4
Creating legacy 0.10.x branch for longer term support -- main branch will become `gufe` refactor
#1211
ijpulidos
opened
1 year ago
1
Store initial and final topologies for all phases -- small molecule pipeline
#1210
ijpulidos
closed
1 year ago
3
AtomMapper fails when scaffolds have radicals
#1209
ijpulidos
opened
1 year ago
1
release notes for 0.10.2
#1208
mikemhenry
closed
1 year ago
3
Using default online analysis interval in GPU repex tests
#1207
ijpulidos
closed
1 year ago
1
enable merge queue
#1206
mikemhenry
closed
1 year ago
0
Write initial initial and final structures in subdir
#1205
ijpulidos
opened
1 year ago
0
Integrate new atom mappers
#1204
ijpulidos
opened
1 year ago
7
Fixes for new openmmtools 0.23.0
#1203
mikemhenry
closed
1 year ago
5
Allow specifying solvent model in input YAML file
#1202
ijpulidos
closed
1 year ago
3
drop 3.8, add 3.11
#1201
mikemhenry
closed
1 year ago
1
Improve docker building
#1200
mikemhenry
closed
1 year ago
5
Document how to control the log level in the CLI
#1198
mikemhenry
closed
1 year ago
2
REST scaling for protein-ligand systems with the CLI
#1197
ijpulidos
opened
1 year ago
2
Next