Commits · a07aace0eff5515a0d5da6e9c1d5a3fb55e066a5 · tsoc / openmm

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20 Jan, 2016 8 commits
- Merge pull request #1354 from peastman/deviceindex · a07aace0
  peastman authored Jan 20, 2016
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Fixed bug in selecting device index
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  a07aace0
- Merge pull request #1348 from rafwiewiora/forcefield_type_wildcard · ab6cabb4
  peastman authored Jan 20, 2016
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Enable wildcard use for Atom Types
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  ab6cabb4
- Fixed bug in selecting device index · 35913c2a
  peastman authored Jan 20, 2016
  
  35913c2a
- fix indent · 4e742ade
  Rafal P. Wiewiora authored Jan 20, 2016
  
  4e742ade
- tests · bd6c5aa9
  Rafal P. Wiewiora authored Jan 20, 2016
  
  bd6c5aa9
- Merge pull request #1353 from jchodera/update-readme · 95e05711
  peastman authored Jan 20, 2016
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Update README.md badges and links
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  95e05711
- Update API docs URLs in README.md · e3582237
  John Chodera (MSKCC) authored Jan 19, 2016
  
  e3582237
- Update badges and URLs on README.md · f92cbe4c
  John Chodera (MSKCC) authored Jan 19, 2016
  
  f92cbe4c
19 Jan, 2016 12 commits
- Merge pull request #1311 from swails/gbparams · 0bdeeb0e
  peastman authored Jan 19, 2016
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Move all of the logic for GB parameter assignment into the new subclasses
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  0bdeeb0e
- Merge pull request #1349 from jchodera/fix-ionic-strength · 5120bb0d
  peastman authored Jan 19, 2016
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Fix error in ionicStrength definition in Modeller.addSolvent()
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  5120bb0d
- Fixed tests · 4b2ef27c
  jchodera authored Jan 19, 2016
  
  4b2ef27c
- Merge remote-tracking branch 'upstream/master' into fix-ionic-strength · 46f62eb2
  jchodera authored Jan 19, 2016
  
  46f62eb2
- Merge pull request #1351 from peastman/fft · 6b3a8337
  peastman authored Jan 19, 2016
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Removed calls to cufftSetCompatibilityMode()
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  6b3a8337
- Fix the AmberCustomGBForce.getStandardParameters and make it work with · f5922dec
  Jason Swails authored Jan 19, 2016
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mm.GBSAOBCForce as well.
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  f5922dec
- Removed calls to cufftSetCompatibilityMode() · cb6a3298
  Peter Eastman authored Jan 19, 2016
  
  cb6a3298
- Fix some forgotten references. · ce661524
  Jason Swails authored Jan 01, 2016
  
  ce661524
- Fix syntax error. · 233b9694
  Jason Swails authored Jan 01, 2016
  
  233b9694
- Remove unnecessary trailing ; · e79f1488
  Jason Swails authored Dec 30, 2015
  
  e79f1488
- Move all of the logic for GB parameter assignment into the new subclasses · fd74112b
  Jason Swails authored Dec 30, 2015
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Previously, parameters were defined in multiple places -- amber_file_parser.py
and charmmpsffile.py.
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  fd74112b
- Number of monovalent ions added is now correctly determined from ionic strength. · d5fa8d74
  jchodera authored Jan 18, 2016
  
  d5fa8d74
18 Jan, 2016 2 commits
- correction · 7e0bd506
  Rafal P. Wiewiora authored Jan 18, 2016
  
  7e0bd506
- enable wildcard use for types · 4f66c0c6
  Rafal P. Wiewiora authored Jan 18, 2016
  
  4f66c0c6
15 Jan, 2016 5 commits
- Merge pull request #1302 from rafwiewiora/pdb_extra_particles · 2acba7ad
  peastman authored Jan 15, 2016
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Allow specification of extra particles in PDB files via element field and extraParticleIdentifier
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  2acba7ad
- fix docstring · ef0ce25a
  Rafal P. Wiewiora authored Jan 15, 2016
  
  ef0ce25a
- Merge pull request #1341 from peastman/checkpoint · 5eb3f8ad
  peastman authored Jan 15, 2016
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Loading a checkpoint marks that positions have been set
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  5eb3f8ad
- Loading a checkpoint marks that positions have been set · 2f5bb780
  Peter Eastman authored Jan 14, 2016
  
  2f5bb780
- Merge pull request #1340 from peastman/amoebagroups · a5d900d1
  peastman authored Jan 14, 2016
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Record force group for AMOEBA forces
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  a5d900d1
14 Jan, 2016 8 commits
- Record force group for AMOEBA forces · 7ccd10ca
  Peter Eastman authored Jan 14, 2016
  
  7ccd10ca
- Merge pull request #1339 from peastman/hydrogens · 34fdeae4
  peastman authored Jan 14, 2016
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Improvements to addHydrogens()
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  34fdeae4
- Merge pull request #1338 from peastman/centroidserialize · c66270ad
  peastman authored Jan 14, 2016
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Fixed a bug in serializing CustomCentroidBondForce
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  c66270ad
- Improvements to addHydrogens() · 4e794b38
  Peter Eastman authored Jan 14, 2016
  
  4e794b38
- Fixed a bug in serializing CustomCentroidBondForce · 202c24d9
  peastman authored Jan 14, 2016
  
  202c24d9
- Merge pull request #1337 from peastman/extrapolated · 71de4b1b
  peastman authored Jan 14, 2016
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AMOEBA extrapolated polarization
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  71de4b1b
- Added extrapolated polarization support to Python and to manual · 49cbc791
  Peter Eastman authored Jan 14, 2016
  
  49cbc791
- CUDA implementation of GK with extrapolated polarization · e47f3ae1
  Peter Eastman authored Jan 13, 2016
  
  e47f3ae1
13 Jan, 2016 1 commit
- Finished CUDA implementation of PME with extrapolated polarization · 3bb595ce
  Peter Eastman authored Jan 13, 2016
  
  3bb595ce
12 Jan, 2016 2 commits
- Continuing CUDA implementation of extrapolated polarization · 6ab144ba
  Peter Eastman authored Jan 12, 2016
  
  6ab144ba
- Merge pull request #1336 from swails/acos · 83408400
  peastman authored Jan 12, 2016
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More acos protections in Amoeba
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  83408400
11 Jan, 2016 2 commits
- Merge pull request #1333 from jchodera/fix-readme · 6fda4b25
  peastman authored Jan 11, 2016
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Remove Jenkins badges from README.md
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  6fda4b25
- Ugh... stop shadowing dot so I can use it as a function. I hate obscure compiler · 103618fb
  Jason Swails authored Jan 11, 2016
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errors.
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  103618fb