Commits · cc920d6aa47318a4e2eb98a55cd14075dd4473be · tsoc / openmm

08 Jan, 2016 1 commit
- clean up extraParticleIdentifier None · cc920d6a
  Rafal P. Wiewiora authored Jan 08, 2016
  
  cc920d6a
16 Dec, 2015 5 commits
- PdbStructure passes element EP to PDBFile, rather than any extraParticleIdentifier · adb707e5
  Rafal P. Wiewiora authored Dec 16, 2015
  
  adb707e5
- fix writeFile for extraParticleIdentifier=None · 89635b86
  Rafal P. Wiewiora authored Dec 16, 2015
  
  89635b86
- add support for extraParticleIdentifier · c8cbc3d5
  Rafal P. Wiewiora authored Dec 16, 2015
  
  c8cbc3d5
- Merge pull request #1300 from rmcgibbo/ccache · 461fcdf0
  peastman authored Dec 15, 2015
```
[CI] Use ccache
```
  461fcdf0
- Add ccache · ed478282
  Robert McGibbon authored Dec 15, 2015
  
  ed478282
15 Dec, 2015 3 commits
- Merge pull request #1299 from peastman/reorder · 6ed5d684
  peastman authored Dec 15, 2015
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Minor optimization
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  6ed5d684
- Minor optimization · 2a02b6f1
  Peter Eastman authored Dec 15, 2015
  
  2a02b6f1
- Merge pull request #1296 from peastman/bugs · cab0faf8
  peastman authored Dec 14, 2015
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Bug fixes
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  cab0faf8
14 Dec, 2015 7 commits
- Bug fixes · 80d41381
  Peter Eastman authored Dec 14, 2015
  
  80d41381
- Merge pull request #1295 from peastman/centroid · 844a91b4
  peastman authored Dec 14, 2015
```
Added serialization proxy for CustomCentroidBondForce
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  844a91b4
- Added serialization proxy for CustomCentroidBondForce · eb943ace
  peastman authored Dec 14, 2015
  
  eb943ace
- Merge pull request #1294 from pandegroup/rmcgibbo-patch-1 · 239dc39e
  peastman authored Dec 14, 2015
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Update CustomHbondForce.h
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  239dc39e
- Merge pull request #1289 from rmcgibbo/appveyor-opencl2 · 5f9e7d01
  peastman authored Dec 14, 2015
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Add OpenCL to Appveyor and fix nosetests
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  5f9e7d01
- Other header updates to bring docs into consistency with function signatures · 90fea164
  Robert T. McGibbon authored Dec 13, 2015
  
  90fea164
- Update CustomHbondForce.h · 322bd639
  Robert T. McGibbon authored Dec 13, 2015
  
  322bd639
12 Dec, 2015 5 commits
- Fix path · 8807d7b4
  Robert T. McGibbon authored Dec 12, 2015
  
  8807d7b4
- Add OpenCL to Appveyor and fix nosetests · a802dfc2
  Robert T. McGibbon authored Dec 10, 2015
  
  a802dfc2
- Merge pull request #1291 from peastman/platformdoc · 4bafde33
  peastman authored Dec 11, 2015
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Minor changes to doxygen comments
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  4bafde33
- Merge pull request #1290 from peastman/energyfix · 3a1936fd
  peastman authored Dec 11, 2015
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Fixed error in energy computation
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  3a1936fd
- Minor changes to doxygen comments · 0af10b15
  peastman authored Dec 11, 2015
  
  0af10b15
11 Dec, 2015 1 commit
- Fixed error in energy computation · 86b2af14
  peastman authored Dec 11, 2015
  
  86b2af14
02 Dec, 2015 1 commit
- Merge pull request #1279 from peastman/nucleic · 4d32047c
  peastman authored Dec 01, 2015
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Support nucleic acids in AMOEBA 2009
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  4d32047c
01 Dec, 2015 1 commit
- Merge pull request #1276 from rafwiewiora/multi_model_conect · 42b7ccd3
  peastman authored Dec 01, 2015
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Add CONECT bonds for multi-model pdb files 
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  42b7ccd3
25 Nov, 2015 1 commit
- add CONECT bonds for multimodel pdb files · a56ba941
  Rafal P. Wiewiora authored Nov 25, 2015
  
  a56ba941
23 Nov, 2015 2 commits
- Merge pull request #1275 from peastman/enforceperiodic · 83cfc856
  peastman authored Nov 23, 2015
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Fixed bug in getState() when enforcing periodic boundary conditions
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  83cfc856
- Fixed bug in getState() when enforcing periodic boundary conditions · 6463111f
  peastman authored Nov 23, 2015
  
  6463111f
21 Nov, 2015 1 commit
- Merge pull request #1273 from peastman/shake · d92e0937
  peastman authored Nov 20, 2015
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Increased SHAKE iterations when positioning extra particles
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  d92e0937
20 Nov, 2015 7 commits
- Increased SHAKE iterations when positioning extra particles · 6bb532ac
  peastman authored Nov 20, 2015
  
  6bb532ac
- Merge pull request #1272 from swails/amber-switching · 40dfdeea
  peastman authored Nov 20, 2015
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Amber switching
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  40dfdeea
- More clarification. · cb2ad95d
  Jason Swails authored Nov 20, 2015
  
  cb2ad95d
- Fix docstring. · 35adccb0
  Jason Swails authored Nov 20, 2015
  
  35adccb0
- Fix unit handling in switchDistance and add tests. · 9e934f69
  Jason Swails authored Nov 20, 2015
  
  9e934f69
- Merge branch 'master' into amber-switching · 1c938ceb
  Jason Swails authored Nov 20, 2015
```
 Conflicts:
	wrappers/python/simtk/openmm/app/amberprmtopfile.py

In fixing the merge conflict, I went ahead and fixed up the switchDistance logic
to match what I did in CharmmPsfFile.
```
  1c938ceb
- Merge pull request #1271 from peastman/gbvi · 167ae8a0
  peastman authored Nov 19, 2015
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Deleted GBVIForce
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  167ae8a0
19 Nov, 2015 3 commits
- Deleted GBVIForce · 14e78600
  Peter Eastman authored Nov 19, 2015
  
  14e78600
- Hopefully finished with supporting nucleotides in AMOEBA · 69d7dc4f
  peastman authored Nov 19, 2015
  
  69d7dc4f
- Fixed bugs that affected nucleotides in AMOEBA · 4daa1acb
  Peter Eastman authored Nov 19, 2015
  
  4daa1acb
17 Nov, 2015 2 commits

Merge pull request #1264 from philiptzou/pull-request-ordered-set-fix · b20c20fe
peastman authored Nov 17, 2015
```
Fix #1213 addInteractionGroup should accept `set` values as parameters
```
b20c20fe

Fix #1213 addInteractionGroup should accept `set` values as parameters. · 43f07a1a

Philip_Tzou authored Nov 17, 2015

apparently SWIG typemaps maps Python's list but not set with std::set.
Instead, Python's `set` is mapped with `std::unordered_set`.

The original code of `swigInputBuilder.py` is kindly in a mess. Too much
lines in a single method `writeMethods` which causes debug becomes
difficult. Also there are a lot of warnings about
[PEP8](https://www.python.org/dev/peps/pep-0008/).

A refactoring in the future may be a good idea.

43f07a1a