Commits · f7b56fdff2722208f98048aeddf3cba93208b94a · tsoc / openmm

20 Jan, 2016 10 commits
- Merge remote-tracking branch 'upstream/master' into forcefield · f7b56fdf
  John Chodera (MSKCC) authored Jan 20, 2016
  
  f7b56fdf
- Merge pull request #1353 from jchodera/update-readme · 95e05711
  peastman authored Jan 20, 2016
```
Update README.md badges and links
```
  95e05711
- Trivial change to re-trigger travis. · a04f3714
  John Chodera (MSKCC) authored Jan 20, 2016
  
  a04f3714
- Fix test · 7aacdeb1
  John Chodera (MSKCC) authored Jan 20, 2016
  
  7aacdeb1
- Add test for parameterizing system using templates built with the help of... · 06b61c6e
  John Chodera (MSKCC) authored Jan 20, 2016
```
Add test for parameterizing system using templates built with the help of getUniqueUnmatchedResidues()
```
  06b61c6e
- Fix import · 4f86aac9
  John Chodera (MSKCC) authored Jan 19, 2016
  
  4f86aac9
- Fix omitted template accumulation. · ce70fa17
  John Chodera (MSKCC) authored Jan 19, 2016
  
  ce70fa17
- Merge remote-tracking branch 'upstream/master' into forcefield · 86d8dbf9
  John Chodera (MSKCC) authored Jan 19, 2016
  
  86d8dbf9
- 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 24 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
```
  0bdeeb0e
- Also return residue templates; add docs. · 818db2b2
  jchodera authored Jan 19, 2016
  
  818db2b2
- Merge pull request #1349 from jchodera/fix-ionic-strength · 5120bb0d
  peastman authored Jan 19, 2016
```
Fix error in ionicStrength definition in Modeller.addSolvent()
```
  5120bb0d
- Fix test · 88d7ee6a
  jchodera authored Jan 19, 2016
  
  88d7ee6a
- Merge remote-tracking branch 'upstream/master' into forcefield · 4d007499
  jchodera authored Jan 19, 2016
  
  4d007499
- 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()
```
  6b3a8337
- Fix the AmberCustomGBForce.getStandardParameters and make it work with · f5922dec
  Jason Swails authored Jan 19, 2016
```
mm.GBSAOBCForce as well.
```
  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
```
Previously, parameters were defined in multiple places -- amber_file_parser.py
and charmmpsffile.py.
```
  fd74112b
- Minor fix for tests. · f1ec09fe
  John Chodera (MSKCC) authored Jan 19, 2016
  
  f1ec09fe
- Minor fix for tests. · eb8d56e0
  John Chodera (MSKCC) authored Jan 19, 2016
  
  eb8d56e0
- Neglected to return bondedToAtom · bdf9cb95
  John Chodera (MSKCC) authored Jan 19, 2016
  
  bdf9cb95
- Fix issue with bond enumeration. · 28c28ead
  John Chodera (MSKCC) authored Jan 19, 2016
  
  28c28ead
- Suppress PDB warnings about duplicate atom names. · 4f352019
  John Chodera (MSKCC) authored Jan 19, 2016
  
  4f352019
- Fix omitted construction of bondedToAtom · dd432501
  John Chodera (MSKCC) authored Jan 19, 2016
  
  dd432501
- Add methods to get unmatched residues without forcefield templates. · a773f1c7
  John Chodera (MSKCC) authored Jan 19, 2016
  
  a773f1c7
- Merge remote-tracking branch 'upstream/master' into forcefield · 39120086
  John Chodera (MSKCC) authored Jan 18, 2016
  
  39120086
- Updates to forcefield. · 87b95319
  John Chodera (MSKCC) authored Jan 18, 2016
  
  87b95319
- Number of monovalent ions added is now correctly determined from ionic strength. · d5fa8d74
  jchodera authored Jan 18, 2016
  
  d5fa8d74
15 Jan, 2016 5 commits
- Merge pull request #1302 from rafwiewiora/pdb_extra_particles · 2acba7ad
  peastman authored Jan 15, 2016
```
Allow specification of extra particles in PDB files via element field and extraParticleIdentifier
```
  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
```
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
```
Record force group for AMOEBA forces
```
  a5d900d1
14 Jan, 2016 1 commit
- Record force group for AMOEBA forces · 7ccd10ca
  Peter Eastman authored Jan 14, 2016
  
  7ccd10ca