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proteneer
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timemachine
Differentiate all the things!
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Adds a margin parameter to builders to ensure boxes are correctly dimensioned everywhere
#1341
badisa
opened
23 hours ago
0
Improve nonbonded decoupling protocol for single topology transformations
#1340
mcwitt
opened
1 week ago
0
Improve Minimization
#1339
badisa
opened
1 week ago
0
Minimize InitialStates only considering fully interacting atoms for the min_cutoff threshold
#1338
badisa
closed
1 week ago
5
Remove redundant definition
#1337
mcwitt
closed
1 week ago
0
Minor improvements to optimize_coordinates
#1336
badisa
closed
1 week ago
0
update to 1.20.3-1ubuntu2.1
#1335
jkausrelay
closed
2 weeks ago
0
Add method to get samples from context without storing to disk
#1334
badisa
closed
2 weeks ago
0
Moves OpenMM imports to function calls
#1333
badisa
closed
3 weeks ago
0
[wip] Don't return cores that will trigger a SingleTopology constructor error
#1332
maxentile
closed
3 weeks ago
2
Fixes Local MD HREX determinism
#1331
badisa
closed
3 weeks ago
0
Log wall time per frame
#1330
mcwitt
closed
3 weeks ago
0
Remove unnecessary array copy in `extract_trajectories_by_replica`
#1329
mcwitt
closed
1 month ago
0
Correct docstring in get_cores
#1328
badisa
closed
1 month ago
0
Increment frame message to be one indexed
#1327
badisa
closed
1 month ago
0
Avoid writing frames to disk only to be read into memory immediately
#1326
badisa
closed
1 month ago
0
Hardcode n_frames_per_iter to 1
#1325
mcwitt
closed
1 month ago
0
Resolve inconsistency between bar_with_bootstrapped_uncertainty and df_and_err_from_u_kln
#1324
badisa
closed
1 month ago
0
Speed up energy decomposition
#1323
badisa
closed
1 month ago
2
Clean up dhfr nonbonded tests
#1322
badisa
closed
1 month ago
1
Fix off-by-one misalignment of permutations and frames in HREX output
#1321
mcwitt
closed
1 month ago
0
Add convenience methods to extract ligand trajectories by replica
#1320
mcwitt
closed
1 month ago
5
Fix nightly test
#1319
mcwitt
closed
1 month ago
1
Remove openmm imports from top level
#1318
badisa
closed
1 month ago
0
Speed-up connected_core MCS by 2-3x
#1317
proteneer
closed
1 month ago
0
Remove HREX replica-state distribution convergence plot
#1316
mcwitt
closed
1 month ago
0
Adds verify_chiral_consistency_of_core to verify cores quickly
#1315
badisa
closed
1 month ago
2
Adds normalized kl divergence metric
#1314
badisa
closed
1 month ago
0
Adopt dummy values for segmented sumexp that compile in latest cub
#1313
badisa
closed
1 month ago
2
Use fast real to int64 conversion for all recent GPUs
#1312
badisa
closed
1 month ago
0
Avoid reading in an invalid sample, triggering an invalid memory access
#1311
badisa
closed
1 month ago
2
Test additional MCS pruning heuristics if `connected_core = True`
#1310
proteneer
closed
1 month ago
2
Reduce cost of u_kl computation in HREX
#1309
mcwitt
closed
1 month ago
0
Add Potential::execute_batch_sparse
#1308
mcwitt
closed
1 month ago
2
Adds Nightly Memcheck job
#1307
badisa
closed
2 months ago
0
Remove test requirements from top level docker
#1306
badisa
closed
2 months ago
0
Switch to uint32 rather than int_ to avoid warning
#1305
badisa
closed
2 months ago
0
Improve memory throughput of atom by atom
#1304
badisa
closed
2 months ago
0
Sample velocities when setting up initial states
#1303
badisa
closed
2 months ago
0
Avoid setting global numpy PRNG seed
#1302
mcwitt
closed
2 months ago
2
Fixes BDExchange nightly test for #1290
#1301
badisa
closed
2 months ago
0
Improve performance of Vacuum Related Kernels
#1300
badisa
closed
2 months ago
1
Update the Water Sampling Determinism tests
#1299
badisa
closed
2 months ago
0
Improve performance of Vacuum related kernels
#1298
badisa
closed
2 months ago
0
Improves performance of Local MD potentials
#1297
badisa
closed
2 months ago
1
Add benchmark for water sampling
#1296
badisa
closed
2 months ago
0
Increase radius of BRD4 test system
#1295
badisa
closed
2 months ago
0
Improve performance of HREX swap moves
#1294
mcwitt
closed
2 months ago
3
Add utility method to emit RDKit mol from SingleTopology classes
#1293
proteneer
closed
2 months ago
0
Add additional dependencies for mypy in pre-commit
#1292
mcwitt
closed
2 months ago
0
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