Commits · 42686c7ac751f97ff079ba83fa1e40b896e54b21 · tsoc / openmm

11 Nov, 2016 4 commits
- More singletons · 42686c7a
  Jason Swails authored Nov 11, 2016
  
  42686c7a
- Fix typo. · 8f8dbd12
  Jason Swails authored Nov 11, 2016
  
  8f8dbd12
- - Add a class to make what are intended to be Singletons really Singletons · 829792ef
  Jason Swails authored Nov 10, 2016
```
- Make Python 2.7 a minimum requirement per pandegroup/openmm#1656
- Make the bond classes as well as other forcefield.py singletons inherit from
  Singleton to make them pickleable
- Make class Bond inherit from namedtuple instead of tuple
```
  829792ef
- Add a test to make sure that the bond types are really singletons. · 311a2cff
  Jason Swails authored Nov 10, 2016
  
  311a2cff
10 Nov, 2016 2 commits
- Created Bond class that can store bond type and order · 7c7b945e
  peastman authored Nov 10, 2016
  
  7c7b945e
- Merge pull request #1665 from peastman/external · b465c982
  peastman authored Nov 10, 2016
```
Added ignoreExternalBonds option to createSystem()
```
  b465c982
09 Nov, 2016 4 commits
- Fixed failing test case · f3ce6720
  peastman authored Nov 09, 2016
  
  f3ce6720
- Added ignoreExternalBonds option to createSystem() · ff55a3a0
  peastman authored Nov 09, 2016
  
  ff55a3a0
- Merge pull request #1664 from peastman/dcd · f968bf99
  peastman authored Nov 09, 2016
```
Fixed error writing a DCD file for a very long trajectory
```
  f968bf99
- Fixed error writing a DCD file for a very long trajectory · 61293829
  peastman authored Nov 09, 2016
  
  61293829
08 Nov, 2016 1 commit
- Merge pull request #1663 from peastman/customswitch · 31c883b3
  peastman authored Nov 08, 2016
```
Fixed bug in switching functions with CustomNonbondedForce
```
  31c883b3
07 Nov, 2016 1 commit
- Fixed bug in switching functions with CustomNonbondedForce · c300870a
  Peter Eastman authored Nov 07, 2016
  
  c300870a
28 Oct, 2016 2 commits
- Merge pull request #1655 from peastman/checkaxis · 04b1a060
  peastman authored Oct 28, 2016
```
Added error checking to axis particle indices
```
  04b1a060
- Added error checking to axis particle indices · ba19d607
  peastman authored Oct 28, 2016
  
  ba19d607
25 Oct, 2016 1 commit
- Merge pull request #1652 from peastman/singular · ff270126
  peastman authored Oct 25, 2016
```
Handle singular matrix in DIIS
```
  ff270126
24 Oct, 2016 2 commits
- Handle singular matrix in DIIS · ca4bbc18
  Peter Eastman authored Oct 24, 2016
  
  ca4bbc18
- Merge pull request #1647 from peastman/polarizationzero · 5f509089
  peastman authored Oct 24, 2016
```
Support multipoles with polarization set to 0
```
  5f509089
20 Oct, 2016 3 commits
- Support multipoles with polarization set to 0 · effb1f57
  Peter Eastman authored Oct 20, 2016
  
  effb1f57
- Merge pull request #1646 from peastman/zonly · 9480ec98
  peastman authored Oct 20, 2016
```
Fixed errors with multipoles set to ZOnly mode
```
  9480ec98
- Fixed errors with multipoles set to ZOnly mode · f6d209af
  Peter Eastman authored Oct 20, 2016
  
  f6d209af
18 Oct, 2016 9 commits
- Merge pull request #1642 from peastman/radius · 1f78252a
  peastman authored Oct 18, 2016
```
Fixed bug computing neighbor list
```
  1f78252a
- Fixed bug in OpenCL as well · 2c47f7b2
  Peter Eastman authored Oct 18, 2016
  
  2c47f7b2
- Fixed bug computing neighbor list · 556dddb6
  Peter Eastman authored Oct 18, 2016
  
  556dddb6
- Merge pull request #1640 from peastman/diis · 5ea8680f
  peastman authored Oct 18, 2016
```
Solve DIIS matrix on GPU
```
  5ea8680f
- Merge pull request #1641 from jchodera/gb-cleanup · d1caf109
  peastman authored Oct 18, 2016
```
Change variable 'q' to 'charge' in custom gb models
```
  d1caf109
- Added a missing fabs() · c0538e1f
  Peter Eastman authored Oct 18, 2016
  
  c0538e1f
- Merge pull request #1639 from jchodera/update-docs · 38d967b2
  peastman authored Oct 18, 2016
```
Update docstrings to specify units and domain for torsions
```
  38d967b2
- Change variable 'q' to 'charge' in custom gb models · d02f75ff
  John Chodera (MSKCC) authored Oct 18, 2016
  
  d02f75ff
- Fix API docs · ef4e38b9
  John Chodera (MSKCC) authored Oct 17, 2016
  
  ef4e38b9
17 Oct, 2016 4 commits
- Solve DIIS matrix on GPU · 805bba93
  Peter Eastman authored Oct 17, 2016
  
  805bba93
- Update theory and API docs with correct dihedral range. · 8ae2ee1b
  jchodera authored Oct 17, 2016
  
  8ae2ee1b
- Merge pull request #1618 from jchodera/fix-mts · e5be7821
  peastman authored Oct 17, 2016
```
Fix precision issue in MTSIntegrator
```
  e5be7821
- Update docstrings of CustomCompoundBondForce and CustomTorsionForce to specify... · 0a1895d3
  jchodera authored Oct 17, 2016
```
Update docstrings of CustomCompoundBondForce and CustomTorsionForce to specify units and domain of torsion
```
  0a1895d3
15 Oct, 2016 3 commits
- Remove noop · 763cbaa1
  John Chodera (MSKCC) authored Oct 15, 2016
  
  763cbaa1
- Add tests of MTS integrator. · d8f96b30
  John Chodera (MSKCC) authored Oct 15, 2016
  
  d8f96b30
- Merge remote-tracking branch 'upstream/master' into fix-mts · 669e314e
  John Chodera (MSKCC) authored Oct 15, 2016
  
  669e314e
14 Oct, 2016 1 commit
- Merge pull request #1632 from peastman/pairs · 388bf972
  peastman authored Oct 14, 2016
```
Fine grained pair list of nonbonded interactions
```
  388bf972
13 Oct, 2016 3 commits
- Merge pull request #1630 from peastman/bug · 064a781f
  peastman authored Oct 13, 2016
```
Fixed bug computing energies without forces
```
  064a781f
- Merge pull request #1631 from jchodera/fix-travis · 89f8a27e
  peastman authored Oct 13, 2016
```
Fix AMD APP SDK path
```
  89f8a27e
- Fix AMD APP SDK path · e9978966
  jchodera authored Oct 13, 2016
  
  e9978966