Commits · 18c9ba5951284721f6fdb3f83c75b375220b9e31 · tsoc / openmm

16 Feb, 2012 2 commits
- CustomIntegrator computed energy incorrectly · 18c9ba59
  Peter Eastman authored Feb 16, 2012
  
  18c9ba59
- Fixed bugs in adding solvent · 663a8db0
  Peter Eastman authored Feb 16, 2012
  
  663a8db0
15 Feb, 2012 2 commits
- Bug fixes to adding constraints when loading AMBER files: compute constrained... · bc157f03
  Peter Eastman authored Feb 15, 2012
```
Bug fixes to adding constraints when loading AMBER files: compute constrained angles correctly, respect the rigidWater flag
```
  bc157f03
- Bug fix · d6a744dd
  Peter Eastman authored Feb 15, 2012
  
  d6a744dd
14 Feb, 2012 3 commits
- OpenCL implementation of multiple time step integrators · 91247209
  Peter Eastman authored Feb 14, 2012
  
  91247209
- Reduced unnecessary force evaluations with multiple time step integrators · 85636c52
  Peter Eastman authored Feb 14, 2012
  
  85636c52
- Created architecture for multiple time step integrators and completed reference implementation · 8ecf9e35
  Peter Eastman authored Feb 14, 2012
  
  8ecf9e35
13 Feb, 2012 1 commit
- Improved rounding behavior when computing the number of ions to add · d817b46b
  Peter Eastman authored Feb 13, 2012
  
  d817b46b
11 Feb, 2012 3 commits
- LocalEnergyMinimizer does not move massless particles · 285a4d88
  Peter Eastman authored Feb 11, 2012
  
  285a4d88
- Finished implementing addHydrogens() · c3ca5fc0
  Peter Eastman authored Feb 11, 2012
  
  c3ca5fc0
- Handle alternate locations in PDB files correctly · c7d32e9c
  Peter Eastman authored Feb 11, 2012
  
  c7d32e9c
10 Feb, 2012 4 commits
- Fixed bug applying constraints for CustomIntegrator · 34bd3ee9
  Peter Eastman authored Feb 10, 2012
  
  34bd3ee9
- ApplyConstraintsKernel did not work correctly · cf7a8bcb
  Peter Eastman authored Feb 10, 2012
  
  cf7a8bcb
- Deleted file with wrong capitalization · d51a7a5c
  Peter Eastman authored Feb 10, 2012
  
  d51a7a5c
- Implementing addHydrogens() · dfdf8328
  Peter Eastman authored Feb 10, 2012
  
  dfdf8328
09 Feb, 2012 1 commit
- Added OPENMM_EXPORT to throwException() declaration for Windows builds · 4ae53b55
  Mark Friedrichs authored Feb 09, 2012
  
  4ae53b55
08 Feb, 2012 2 commits
- Correct reference · 3836a29f
  Mark Friedrichs authored Feb 08, 2012
  
  3836a29f
- Implemented addSolvent() · 15c272fd
  Peter Eastman authored Feb 08, 2012
  
  15c272fd
07 Feb, 2012 1 commit
- Removed debug code · de404267
  Mark Friedrichs authored Feb 07, 2012
  
  de404267
02 Feb, 2012 4 commits
- Take virtual sites into account when identifying molecules · 71ec749c
  Peter Eastman authored Feb 02, 2012
  
  71ec749c
- Replaced TIP4P with TIP4P-Ew · b593e034
  Peter Eastman authored Feb 02, 2012
  
  b593e034
- PdbFile and AmberInpcrdFile can return values as Numpy arrays · e2d8c16e
  Peter Eastman authored Feb 02, 2012
  
  e2d8c16e
- Created Modeller class. Two modeling methods are currently supported:... · deb55264
  Peter Eastman authored Feb 02, 2012
```
Created Modeller class.  Two modeling methods are currently supported: deleteWater() and convertWater()
```
  deb55264
01 Feb, 2012 1 commit
- Use PDB 3.0 nomenclature for the Topology created by AmberPrmtopFile · df60bf0d
  Peter Eastman authored Feb 01, 2012
  
  df60bf0d
31 Jan, 2012 3 commits
- Fixed bug when RPMDIntegrator uses more than 32 beads · 6299521b
  Peter Eastman authored Jan 31, 2012
  
  6299521b
- LocalEnergyMinimizer works with virtual sites · f30ddfa4
  Peter Eastman authored Jan 31, 2012
  
  f30ddfa4
- Added index bounds checking to lots of methods · a566a074
  Peter Eastman authored Jan 31, 2012
  
  a566a074
30 Jan, 2012 1 commit
- Fixed error in wrapping of arguments that are maps · 12daada5
  Peter Eastman authored Jan 30, 2012
  
  12daada5
27 Jan, 2012 2 commits
- Renamed math functions in Cuda kernels to single-precision equivalent [cos() -> cosf()] · 470c9b7f
  Mark Friedrichs authored Jan 27, 2012
  
  470c9b7f
- Tony's optimizations to reduce local memory use · fed50628
  Peter Eastman authored Jan 27, 2012
  
  fed50628
26 Jan, 2012 3 commits
- ForceField support TIP4P and TIP5P · 2dd09317
  Peter Eastman authored Jan 26, 2012
  
  2dd09317
- More fixes to compilation errors · 274be989
  Peter Eastman authored Jan 26, 2012
  
  274be989
- Tony's changes to error handling in the CUDA platform so it throws exceptions... · 55081e21
  Peter Eastman authored Jan 26, 2012
```
Tony's changes to error handling in the CUDA platform so it throws exceptions instead of calling exit()
```
  55081e21
25 Jan, 2012 2 commits
- Tony's changes to fix errors on Windows · 832794f5
  Peter Eastman authored Jan 25, 2012
  
  832794f5
- OpenCL implementation of virtual sites · 94ecc958
  Peter Eastman authored Jan 25, 2012
  
  94ecc958
23 Jan, 2012 2 commits
- Define both __div__ and __truediv__ to work on all Python versions · bfc1b529
  Peter Eastman authored Jan 23, 2012
  
  bfc1b529
- Changes to support Python 3 · d648613b
  Peter Eastman authored Jan 23, 2012
  
  d648613b
20 Jan, 2012 2 commits
- Eliminated nested classes, since SWIG didn't handle them well · d1793e5a
  Peter Eastman authored Jan 20, 2012
  
  d1793e5a
- Added missing units descriptions for virtual sites · f728d2f6
  Peter Eastman authored Jan 20, 2012
  
  f728d2f6
19 Jan, 2012 1 commit
- Implemented virtual sites for reference platform · fd01aa58
  Peter Eastman authored Jan 19, 2012
  
  fd01aa58