Commits · 285a4d88eeabdd162db49370e39e9c4c935da999 · tsoc / openmm

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
18 Jan, 2012 2 commits
- Revised the virtual site API to fix some problems with it · cbd45dca
  Peter Eastman authored Jan 18, 2012
  
  cbd45dca
- Created API for virtual sites · 6074e2e1
  Peter Eastman authored Jan 18, 2012
  
  6074e2e1
14 Jan, 2012 1 commit
- Bug fix to previous bug fix · b0bda3a1
  Peter Eastman authored Jan 14, 2012
  
  b0bda3a1
13 Jan, 2012 3 commits
- Fixed bug in CustomIntegrator when atoms get reordered · 69812ad7
  Peter Eastman authored Jan 13, 2012
  
  69812ad7
- Deleted a file that is no longer used. · 43e57ba0
  Peter Eastman authored Jan 13, 2012
  
  43e57ba0
- Tony Tye's optimizations to sorting. Also a couple of other very minor fixes. · c35407a8
  Peter Eastman authored Jan 13, 2012
  
  c35407a8
12 Jan, 2012 2 commits
- Implemented per-DOF uniform random numbers for OpenCL. Also fixed some bugs... · 052aea3e
  Peter Eastman authored Jan 12, 2012
```
Implemented per-DOF uniform random numbers for OpenCL.  Also fixed some bugs in getting and setting per-DOF variables.
```
  052aea3e
- Optimizations to CustomIntegrator: sum energy on the device, merge kernels when possible · 0d5f265c
  Peter Eastman authored Jan 12, 2012
  
  0d5f265c