Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / choderalab/yank issues and pull requests
#1304 - Silent GAFF2 failures can happen easily
Issue -
State: open - Opened by simonaxelrod about 1 year ago
#1303 - Question: How to measure simulation time and how much is necessary?
Issue -
State: open - Opened by sammun-insitro over 1 year ago
#1302 - Issue in Yank's calls to OpenMMTools MultiStateReporter
Issue -
State: open - Opened by sukritsingh over 1 year ago
#1301 - support for python 3.10?
Issue -
State: open - Opened by zhang-ivy over 1 year ago
- 2 comments
#1300 - problem during absolute binding energy calculation
Issue -
State: open - Opened by mayank-kohli over 1 year ago
- 3 comments
#1299 - Failures due to API changes in `openmmtools`
Issue -
State: closed - Opened by mattwthompson over 1 year ago
- 3 comments
#1298 - NetCDF upstream changes breaking Yank (and can't update OpenMMtools)
Issue -
State: open - Opened by sukritsingh over 1 year ago
#1297 - Issue with Ligand Coordinates During Absolute-Binding Free Energy
Issue -
State: closed - Opened by davidcooper7 over 1 year ago
#1296 - multichain receptor for 'restrained_receptor_atoms'
Issue -
State: closed - Opened by smutao over 1 year ago
#1295 - I got the following error.
Issue -
State: open - Opened by VirtualChemist over 1 year ago
- 6 comments
#1294 - pymbar 4 compatibility
Issue -
State: open - Opened by j-wags almost 2 years ago
- 1 comment
#1293 - Load() missing one argument
Issue -
State: open - Opened by RishalAggarwal almost 2 years ago
#1292 - Free energy of solvation for charged ligand
Issue -
State: open - Opened by moradza almost 2 years ago
#1291 - The periodic box size has decreased to less than twice the nonbonded cutoff
Issue -
State: open - Opened by vemaparna about 2 years ago
#1290 - Update CI
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
#1289 - a error about antecamber
Issue -
State: open - Opened by kingljy0818 about 2 years ago
- 5 comments
#1288 - Yank installation Python3.10 import error
Issue -
State: open - Opened by JonaTheHutt about 2 years ago
- 1 comment
#1287 - Migrate thermodynamic trailblazing to openmmtools
Issue -
State: open - Opened by jchodera about 2 years ago
Labels: refactoring
#1286 - Fix/support python 310
Pull Request -
State: open - Opened by mikemhenry about 2 years ago
- 4 comments
#1285 - pin pymbar to stay on 3.x version
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
- 1 comment
#1284 - Add Python 3.9 and 3.10 to CI matrix
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 4 comments
#1283 - extend on resume
Pull Request -
State: open - Opened by jfennick about 2 years ago
- 1 comment
#1282 - generate_free_energy() fails because standard state correction is missing from the reporter
Issue -
State: open - Opened by zhang-ivy about 2 years ago
- 1 comment
Labels: bug, Priority high
#1281 - Cannot apply the restraint. No receptor-ligand complex could be found.
Issue -
State: open - Opened by j-kedzierski about 2 years ago
- 1 comment
#1280 - Issues about the calculation of solvation free energy in organic solvent
Issue -
State: open - Opened by Dropletsimuli about 2 years ago
#1279 - Yank analysis error
Issue -
State: closed - Opened by kingljy0818 over 2 years ago
- 7 comments
#1278 - difference in experimental and calculated binding free energy for p-xylene -T4Lysozyme example
Issue -
State: open - Opened by vemaparna over 2 years ago
- 6 comments
#1277 - Is it possible to use enhanced sampling algorithms such as REST/REST2?
Issue -
State: open - Opened by jackzzs over 2 years ago
- 1 comment
#1276 - T4 lysozyme example with implicit solvent runs out of memory when lots of memory appears to be available
Issue -
State: open - Opened by therealchrisneale over 2 years ago
#1275 - t4 lysozyme tutorial with implicit solvent appears to hang at first instance of execute _propagate_replica()
Issue -
State: open - Opened by therealchrisneale over 2 years ago
Labels: bug
#1274 - conda yank install fails while attempting to create symbolic link in root while requesting non-root install
Issue -
State: closed - Opened by therealchrisneale over 2 years ago
- 1 comment
#1273 - Windows CI is failing
Issue -
State: closed - Opened by mjw99 over 2 years ago
- 1 comment
#1272 - Updated docker image for YANK
Issue -
State: open - Opened by mmagithub over 2 years ago
- 11 comments
#1271 - Add CITATION.cff file
Issue -
State: open - Opened by mikemhenry over 2 years ago
#1270 - Update continuous integration
Issue -
State: open - Opened by jchodera over 2 years ago
Labels: testing
#1269 - Check attributes accessed in ExperimentAnalyzer.__del__
Issue -
State: open - Opened by lilyminium over 2 years ago
#1268 - Update yaml loader in analyze.py
Pull Request -
State: open - Opened by lilyminium over 2 years ago
- 1 comment
#1267 - Stable minimization
Pull Request -
State: open - Opened by jfennick over 2 years ago
- 2 comments
#1266 - Protocol to mutate a chemical?
Issue -
State: open - Opened by chabi-fin over 2 years ago
#1265 - YANK analyze error
Issue -
State: open - Opened by MehreenZaka over 2 years ago
- 2 comments
#1264 - yank-example-hydration-phenol-Analysis-error
Issue -
State: open - Opened by owenustc over 2 years ago
- 1 comment
#1263 - Update for new OpenMM Namespace
Pull Request -
State: open - Opened by mikemhenry almost 3 years ago
- 5 comments
#1262 - how to get openMM yank free energy per time
Issue -
State: open - Opened by Byun-jinyoung almost 3 years ago
#1261 - Platform-specific energy differences with OpenMM 7.5.1 vs 7.6
Issue -
State: closed - Opened by mattwthompson almost 3 years ago
- 9 comments
#1260 - Module not found after yank update
Issue -
State: open - Opened by gsabbih6 almost 3 years ago
- 6 comments
#1259 - Examples and own tests are not working: Stuck at file not found
Issue -
State: open - Opened by gsabbih6 almost 3 years ago
#1258 - Removed travis CI config file
Pull Request -
State: closed - Opened by mikemhenry about 3 years ago
#1257 - Add feature to automatically select the alchemical ion with largest distance
Pull Request -
State: open - Opened by evohringer about 3 years ago
#1256 - NetCDF: HDF error
Issue -
State: open - Opened by jslim-furame about 3 years ago
- 2 comments
#1255 - ligand position after trailblazing
Issue -
State: open - Opened by isjoung about 3 years ago
#1254 - Can yank be used to calculate the binding energy of proteins and peptides?
Issue -
State: open - Opened by dxli75 over 3 years ago
- 2 comments
#1253 - yank found unknown parameter number_of_iterations in all examples. I changed nothing, just running
Issue -
State: open - Opened by dxli75 over 3 years ago
- 2 comments
Labels: bug, documentation, examples
#1252 - CRITICAL: Experiment NaN
Issue -
State: open - Opened by sadafrani6 over 3 years ago
- 2 comments
#1251 - Cannot find counterions for region {}: Automatic pipeline does not recognize ion ligands/solutes
Issue -
State: open - Opened by ShahbazQalandar over 3 years ago
- 11 comments
Labels: bug
#1250 - Prolonging simulation is not improving number of decorrelated samples
Issue -
State: open - Opened by Eli-VDB over 3 years ago
#1249 - REMD Performance
Issue -
State: open - Opened by shitanshu-cell almost 4 years ago
- 4 comments
#1248 - Error with reading yaml file
Issue -
State: open - Opened by Byun-jinyoung almost 4 years ago
- 3 comments
#1247 - Parallel simulation using slurm queue
Issue -
State: open - Opened by jslim-furame almost 4 years ago
- 3 comments
#1246 - Using yank for calculation of mixing free energy
Issue -
State: open - Opened by Eli-VDB almost 4 years ago
- 3 comments
#1245 - Tests are failing
Issue -
State: open - Opened by jaimergp almost 4 years ago
#1244 - Add GHA CI
Pull Request -
State: closed - Opened by jaimergp almost 4 years ago
- 1 comment
#1243 - Setting problem during absolute binding energy calculation (maybe in complex phase...?)
Issue -
State: open - Opened by Byun-jinyoung almost 4 years ago
- 2 comments
#1242 - hydration free energy of a molecule with Yank
Issue -
State: open - Opened by avdisalem about 4 years ago
- 3 comments
#1241 - AttributeError: module 'simtk.openmm.app.forcefield' has no attribute '_matchResidue'
Issue -
State: open - Opened by tengjieksee about 4 years ago
- 1 comment
#1240 - How to use yank for peptide-protein binding?
Issue -
State: open - Opened by aizvorski about 4 years ago
- 1 comment
#1239 - GPU compute mode
Issue -
State: open - Opened by abazabaaa about 4 years ago
#1238 - NAN issue in hydration free energy calculation
Issue -
State: open - Opened by kexul about 4 years ago
#1237 - Question about YANK restrains
Issue -
State: open - Opened by mmagithub about 4 years ago
#1236 - Hydration free energy protocol does not turn off steric interaction in vacuum
Issue -
State: closed - Opened by isjoung about 4 years ago
- 2 comments
#1235 - CUDA problem
Issue -
State: closed - Opened by mmagithub about 4 years ago
- 5 comments
#1234 - yank analyze error in restraint energy calculation
Issue -
State: closed - Opened by isjoung over 4 years ago
- 5 comments
#1233 - IndexError: invalid index to scalar variable.
Issue -
State: closed - Opened by aysegulcayir over 4 years ago
- 4 comments
#1232 - Fix miniconda install in travis tests
Pull Request -
State: closed - Opened by jchodera over 4 years ago
- 1 comment
#1231 - Errors with analyse report
Issue -
State: open - Opened by kadiliissaar over 4 years ago
#1230 - Could not find t0 or t0 found; using initial t0 = 4908 instead of 1
Issue -
State: open - Opened by kingljy0818 over 4 years ago
#1229 - Which method combination is equal rank comparing with the FEP+ in the yank benchmark c-Met_hinge_binders?
Issue -
State: open - Opened by kingljy0818 over 4 years ago
#1228 - CRITICAL: Experiment NaN !
Issue -
State: open - Opened by kingljy0818 over 4 years ago
- 5 comments
#1227 - Incorporate QM into ligand parameterization pipeline
Issue -
State: open - Opened by tantrev over 4 years ago
- 7 comments
#1226 - Binding pose prediction
Issue -
State: open - Opened by daveminh over 4 years ago
#1225 - How to configure the alchemical_path of complex and solvent of protocol parameter in *.yaml
Issue -
State: open - Opened by kingljy0818 over 4 years ago
#1224 - dcdplugin) Could not access file 'LZ02-mertk-explicit-output/experiments/trailblaze/complex/coordinates.dcd'.
Issue -
State: closed - Opened by kingljy0818 over 4 years ago
- 7 comments
#1223 - How to configure yank script when the receptor includes coenzyme
Issue -
State: open - Opened by kingljy0818 over 4 years ago
- 4 comments
#1222 - How to enable the parallel mode in two gpus server
Issue -
State: open - Opened by kingljy0818 over 4 years ago
- 4 comments
#1221 - Simulations of molecular melt
Issue -
State: closed - Opened by kadiliissaar over 4 years ago
- 3 comments
#1220 - Possible issue with net_charge assignment from yaml with antechamber
Issue -
State: closed - Opened by mjw99 over 4 years ago
- 4 comments
#1219 - [WIP] add support for relative binding free energies
Pull Request -
State: open - Opened by ajsilveira over 4 years ago
#1218 - NaN encountered with hydration example in document.
Issue -
State: closed - Opened by kexul over 4 years ago
- 2 comments
#1217 - Solubility
Issue -
State: closed - Opened by kadiliissaar over 4 years ago
- 1 comment
#1216 - pinning pymbar version
Pull Request -
State: closed - Opened by hannahbrucemacdonald over 4 years ago
- 1 comment
#1214 - Trailblazing analysis error
Issue -
State: closed - Opened by mjw99 over 4 years ago
- 12 comments
#1211 - Use Open Force Field parameters for ligands
Issue -
State: open - Opened by daveminh over 4 years ago
- 20 comments
#1207 - Added support for CHARMM-format input files (psf/pdb and a list of pr…
Pull Request -
State: closed - Opened by jeffcomer over 4 years ago
- 7 comments
#1205 - pymbar error!
Issue -
State: closed - Opened by sawstory over 4 years ago
- 2 comments
#1182 - Binding site identification?
Issue -
State: open - Opened by jadeshi about 5 years ago
- 2 comments
#1152 - yaml.load issues
Issue -
State: open - Opened by jchodera over 5 years ago
- 6 comments
#1130 - MPI bug when multiple GPUs are used per calculation
Issue -
State: closed - Opened by HershGupta404 over 5 years ago
- 8 comments
Labels: bug, repex, critical
#1083 - Failure to set up a single molecule terminates entire MPI calculation
Issue -
State: open - Opened by jchodera about 6 years ago
- 1 comment
Labels: enhancement, error handling
#760 - Add CHARMM input scheme
Issue -
State: closed - Opened by leelasd about 7 years ago
- 12 comments
Labels: enhancement
#547 - Add osx travis branch
Pull Request -
State: closed - Opened by jchodera almost 8 years ago
- 10 comments
#502 - Performance tuning parameters like number of iterations and replicas
Issue -
State: closed - Opened by jlerche about 8 years ago
- 5 comments