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proteneer
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timemachine
Differentiate all the things!
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Add plotting to benchmarks
#1375
badisa
closed
18 hours ago
0
Removes code that assumes ordering of potentials
#1374
badisa
closed
2 hours ago
0
Prefer a more terse way of converting vectors to numpy arrays
#1373
badisa
closed
4 days ago
1
Remove L-W ixn group and merge w/P-L group
#1372
jkausrelay
closed
1 week ago
2
Removes Neighborlist sync from Nonbonded potentials
#1371
badisa
closed
1 day ago
1
Release GIL on pybind calls to Context
#1370
badisa
opened
1 week ago
0
Task/combined vacuum sims
#1369
badisa
closed
1 week ago
0
Adds test that verifies Neighborlist Tile Density
#1368
badisa
closed
5 hours ago
0
Remove stale conda channel
#1367
badisa
closed
2 weeks ago
0
Assert that states differ only in their parameters
#1366
mcwitt
closed
1 day ago
0
Improve ordering of Local MD potentials
#1365
badisa
closed
1 week ago
1
Remove guard threshold from local minimize
#1364
badisa
closed
3 weeks ago
0
Add ring_forming_breaking_count metric
#1363
badisa
closed
3 weeks ago
14
Clean up atom mapping code a bit
#1362
badisa
closed
3 weeks ago
0
Relax element coverage restriction
#1361
maxentile
opened
1 month ago
0
Refactor chiral restraint setup to avoid repeated work
#1360
mcwitt
closed
4 weeks ago
0
Correctly report nodes visited
#1359
badisa
closed
1 month ago
0
Speed up and refactor chiral checks
#1358
proteneer
closed
1 month ago
1
get_cores raises exception when total nodes visits exceed max_visits and no cores are generated
#1357
badisa
closed
1 month ago
5
Add option disallowing atom mappings with no chirally-valid dummy anchor assignment
#1356
proteneer
closed
1 month ago
4
Fixes Free Energy benchmarks
#1355
badisa
closed
1 month ago
0
Move template instantiation to cu file instead of header
#1354
tkramer-motion
closed
1 month ago
0
Move template instantiation to cu file instead of header
#1353
tkramer-motion
closed
1 month ago
0
Move template instantiation to cu file instead of header
#1352
tkramer-motion
closed
1 month ago
1
Add failing test case of minimization
#1351
badisa
closed
1 month ago
0
Add utility to get trajectories by state
#1350
badisa
closed
1 month ago
0
Add atom mapping arguments to restrict the number of connected components in the core
#1349
mcwitt
closed
1 month ago
0
Fixes conditional that triggered warning incorrectly
#1348
badisa
closed
1 month ago
0
Add lambda schedule tuned to Bisection
#1347
badisa
closed
1 month ago
4
Modified Minimization while keeping number of host atoms constant
#1346
badisa
closed
1 month ago
0
Revert "Modify Minimization to avoid minimizing while mols are non-in…
#1345
badisa
closed
1 month ago
0
Fixes bar_with_pessimistic_uncertainty convergence error
#1344
badisa
closed
1 month ago
0
[WIP] Stricter chiral check in _get_cores_impl
#1343
maxentile
closed
1 month ago
1
Perf/verify_chiral_consistency_of_core
#1342
maxentile
closed
1 month ago
4
Adds a margin parameter to builders to ensure boxes are correctly dimensioned everywhere
#1341
badisa
closed
1 month ago
0
Improve nonbonded decoupling protocol for single topology transformations
#1340
mcwitt
closed
1 month ago
0
Modify Minimization to avoid minimizing while mols are non-interacting
#1339
badisa
closed
1 month ago
0
Minimize InitialStates only considering fully interacting atoms for the min_cutoff threshold
#1338
badisa
closed
2 months ago
5
Remove redundant definition
#1337
mcwitt
closed
2 months ago
0
Minor improvements to optimize_coordinates
#1336
badisa
closed
2 months ago
0
update to 1.20.3-1ubuntu2.1
#1335
jkausrelay
closed
2 months ago
0
Add method to get samples from context without storing to disk
#1334
badisa
closed
2 months ago
0
Moves OpenMM imports to function calls
#1333
badisa
closed
2 months ago
0
[wip] Don't return cores that will trigger a SingleTopology constructor error
#1332
maxentile
closed
2 months ago
2
Fixes Local MD HREX determinism
#1331
badisa
closed
2 months ago
0
Log wall time per frame
#1330
mcwitt
closed
2 months ago
0
Remove unnecessary array copy in `extract_trajectories_by_replica`
#1329
mcwitt
closed
3 months ago
0
Correct docstring in get_cores
#1328
badisa
closed
3 months ago
0
Increment frame message to be one indexed
#1327
badisa
closed
3 months ago
0
Avoid writing frames to disk only to be read into memory immediately
#1326
badisa
closed
3 months ago
0
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