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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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Backport openfe fixes for context deletion
#1196
ijpulidos
closed
1 year ago
1
REST max temperature from CLI
#1195
ijpulidos
opened
1 year ago
2
[HybridTopologyFactory] `CustomNonbondedForce` cutoff doesn't match `NonBondedForce`
#1194
IAlibay
closed
1 year ago
4
[HybridTopologyFactory] Copying virtual sites from old/new systems to hybrid system leads to exception
#1193
IAlibay
opened
1 year ago
2
[CLI] no entry point for non-tip3p solvation model
#1192
IAlibay
closed
1 year ago
2
Support for cofactor-bound proteins?
#1191
sukritsingh
opened
1 year ago
1
Update comments in `RESTCapableHybridTopologyFactory`
#1189
zhang-ivy
closed
1 year ago
1
Fix RESTTopologyFactory test
#1188
zhang-ivy
closed
1 year ago
1
Move non-alchemical REST system code to openmmtools
#1187
zhang-ivy
opened
1 year ago
0
Skip failing openmm 8 tests
#1186
mikemhenry
closed
1 year ago
4
change default to none
#1185
mikemhenry
closed
1 year ago
4
Run complete protein-ligand benchmark set with openff-2.1.0rc1 to test benchmark scripts
#1184
jchodera
opened
1 year ago
0
Update benchmarks scripts to run entire protein-ligand benchmarks set
#1183
jchodera
opened
1 year ago
1
Integrate OpenFF / OpenFE protein loaders so that entire system has Molecule representations
#1182
jchodera
opened
1 year ago
2
Update examples to openff-2.1.0rc1
#1181
jchodera
opened
1 year ago
0
Migrate solute-only trajectory writing from NetCDF to XTC
#1180
jchodera
opened
1 year ago
0
Make solute-only trajectory writing optional
#1179
jchodera
closed
1 year ago
3
add caching
#1178
mikemhenry
closed
1 year ago
2
Evaluating unit test coverage; filling in coverage where needed
#1177
dotsdl
closed
1 year ago
11
print perses version on startup
#1176
mikemhenry
closed
1 year ago
1
Make sure logging messages stream to stdout
#1175
ijpulidos
closed
1 year ago
2
use python executable from env
#1174
mikemhenry
closed
1 year ago
3
Support pymbar 4
#1173
mikemhenry
closed
1 year ago
6
`out-solvent.nc` is larger than `out-complex.nc`
#1172
JenkeScheen
closed
1 year ago
2
need a data model that contains essential information of a calculation
#1171
JenkeScheen
opened
1 year ago
7
[DNM] test new openmmtools version
#1170
mikemhenry
closed
1 year ago
5
use `False` for reassign velocities in `ProteinMutationExecutor` docstring example.
#1169
ijpulidos
closed
1 year ago
4
Update docstring example for PointMutationExecutor
#1168
zhang-ivy
closed
1 year ago
1
[DNM] hack to allow undefined stero when mapping
#1167
mikemhenry
closed
1 year ago
3
Include cloudpathlib as requirement in meta.yaml
#1166
craabreu
closed
1 year ago
2
only run dev with newest python version
#1165
mikemhenry
closed
1 year ago
5
Avoid testing non-examples in CI
#1164
ijpulidos
closed
1 year ago
2
fix issue with logic, add debug statements
#1163
mikemhenry
closed
1 year ago
1
update release process
#1162
mikemhenry
closed
1 year ago
1
Mapping/parameterization issue
#1161
viktorbelay
opened
1 year ago
9
Double check usage of `openmmtools` `FireMinimizer`
#1160
ijpulidos
opened
1 year ago
0
remove outdated recipe
#1159
mikemhenry
closed
1 year ago
1
Use bootstrapping by default
#1158
ijpulidos
opened
1 year ago
0
Serialized XML objects in small molecule pipeline have the wrong extension
#1157
ijpulidos
closed
1 year ago
3
List of input smiles as input for `RelativeFEPSetup`
#1156
ijpulidos
opened
1 year ago
0
`RelativeFEPSetup` cannot handle list of smiles as input ligands
#1155
ijpulidos
opened
1 year ago
0
Overhaul perses writing of topology information
#1154
jchodera
closed
1 year ago
2
Questions about mapping
#1153
SZhang66
closed
1 year ago
6
Expand GPU instances or pick new ones for GPU CI
#1152
mikemhenry
closed
1 year ago
4
resolves issue #1150
#1151
mikemhenry
closed
1 year ago
1
Fix resume tests
#1150
ijpulidos
closed
1 year ago
0
Remove basic config
#1149
ijpulidos
closed
1 year ago
1
switch to using openmm rc
#1148
mikemhenry
closed
1 year ago
3
Test Newest OpenMM Release Candidate
#1147
mikemhenry
closed
1 year ago
2
Document Release Process
#1146
mikemhenry
closed
1 year ago
0
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