Commits · 801c43ee422da26aeca82f74a3dd201e53f37d2a · tsoc / openmm

02 Mar, 2012 2 commits
- Throw exception if the box size is reduced to less than twice the cutoff · 801c43ee
  Peter Eastman authored Mar 02, 2012
  
  801c43ee
- Bug fix · 1bcdd3e2
  Peter Eastman authored Mar 02, 2012
  
  1bcdd3e2
28 Feb, 2012 4 commits
- Made test case slightly more tolerant, since SETTLE can introduce small velocity errors · 7401af02
  Peter Eastman authored Feb 28, 2012
  
  7401af02
- API wrappers are marked as depending on the XSLT files that generate them... · 366d10f7
  Peter Eastman authored Feb 28, 2012
```
API wrappers are marked as depending on the XSLT files that generate them (Mike Garrahan's patch to bug 1625).
```
  366d10f7
- Optimizations to SETTLE · caa4fc5a
  Peter Eastman authored Feb 28, 2012
  
  caa4fc5a
- Mike Garrahan's fix to bug 1594 (set and get not working on Fortran arrays) · 5d9219ec
  Peter Eastman authored Feb 28, 2012
  
  5d9219ec
27 Feb, 2012 1 commit
- Allow boxSize argument to be a list or tuple instead of a Vec3 · 0dd32915
  Peter Eastman authored Feb 27, 2012
  
  0dd32915
25 Feb, 2012 1 commit
- Fixed Python wrapper for CustomIntegrator::getPerDofVariable() · d2a6f00c
  Peter Eastman authored Feb 25, 2012
  
  d2a6f00c
24 Feb, 2012 2 commits
- Fixed bugs in CustomIntegrator, including incorrect examples of velocity verlet with constraints · 7b383c7e
  Peter Eastman authored Feb 24, 2012
  
  7b383c7e
- Reimplemented SETTLE velocity constraints with a different algorithm. The old... · dee35ab2
  Peter Eastman authored Feb 24, 2012
```
Reimplemented SETTLE velocity constraints with a different algorithm.  The old one produced incorrect results.
```
  dee35ab2
22 Feb, 2012 2 commits
- Added missing units for cases when temperature_factor is absent · 6bfe2d8b
  Mark Friedrichs authored Feb 22, 2012
  
  6bfe2d8b
- Set default tolerance for mutual induced dipoles to 1.0e-2 -- the value recommended by Jay · 91eeb088
  Mark Friedrichs authored Feb 22, 2012
  
  91eeb088
21 Feb, 2012 1 commit
- Fixed error in applying constraints · a73e6132
  Peter Eastman authored Feb 21, 2012
  
  a73e6132
18 Feb, 2012 2 commits
- Documentation updates for new featuers in 4.1 · 4cd3207e
  Peter Eastman authored Feb 18, 2012
  
  4cd3207e
- getState() can specify which force groups to use · 1595bb7b
  Peter Eastman authored Feb 18, 2012
  
  1595bb7b
17 Feb, 2012 1 commit
- Modeller supports SPC/E water · 1878512f
  Peter Eastman authored Feb 17, 2012
  
  1878512f
16 Feb, 2012 3 commits
- Support 4 and 5 site water when loading prmtop files · 4412050a
  Peter Eastman authored Feb 16, 2012
  
  4412050a
- 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