choderalab perses issues

choderalab / perses

Experiments with expanded ensembles to explore chemical space

http://perses.readthedocs.io

MIT License

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issues

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IndexError with `_vacdg_history` if there is no vacuum trajectory

#1247 slochower opened 3 months ago
3
Improved reporting and state detection when passing tautomers as `old_residue`

#1246 sukritsingh opened 3 months ago
0
Retrieving exact topology used for an endpoint in a relative transformation

#1245 slochower closed 3 months ago
11
Update README?

#1244 zhang-ivy opened 7 months ago
1
[DNM] Test/openmm 8.1.0rc1

#1243 mikemhenry closed 7 months ago
10
[DNM] Test openmm 8.1 release candidate

#1242 ijpulidos closed 8 months ago
3
Allow specification of mapping dictionary in the pipeline

#1241 ijpulidos opened 8 months ago
0
[DNM] test openmm 8.1

#1240 mikemhenry closed 8 months ago
2
Fix incorrect implementation of logsumexp

#1239 mikemhenry closed 9 months ago
1
Fix incorrect implementation of logsumexp

#1238 badisa closed 9 months ago
6
Test new open ffmast fix

#1237 mikemhenry opened 10 months ago
6
Change log for 0.10.3 release

#1236 mikemhenry closed 10 months ago
2
0.10.x merge into main

#1235 mikemhenry closed 10 months ago
6
Fix spectator support

#1233 ijpulidos closed 10 months ago
6
Error with spectator ligands

#1232 arjun-nufc closed 5 months ago
8
Support for use of custom force fields (e.g., one generated from openff-bespokefit)

#1231 arjun-nufc closed 5 months ago
5
Fix/issue 1194

#1230 mikemhenry closed 11 months ago
7
Fix/issue 1196

#1229 mikemhenry closed 11 months ago
1
MPI example with dipeptide mutation

#1228 ijpulidos closed 11 months ago
1
Realtime analysis interval to default to checkpoint interval

#1227 ijpulidos closed 11 months ago
2
Allow user to specify list of atom indices to override default behavior for selecting the REST region

#1226 zhang-ivy opened 11 months ago
0
Fix potential bug in counterion implementation: get_water_indices()

#1225 zhang-ivy opened 11 months ago
0
Adapt MPi example with perses at least for protein mutation

#1224 ijpulidos closed 10 months ago
1
Clean examples -- CLI protein-ligand example for Tyk2

#1223 ijpulidos closed 11 months ago
1
Protein mutation protocol for alchemiscale

#1222 ijpulidos opened 12 months ago
1
Migrate from PDB to PDBx/mmcif

#1221 ijpulidos opened 12 months ago
1
Make `offline-freq` be the same as `checkpoint_interval` by default

#1220 jthorton closed 10 months 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 12 months 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 12 months 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
Backport openfe fixes for context deletion

#1196 ijpulidos closed 10 months ago
1