Commits · db9528ca08ca1ab063564d8aaf83410f899f9ba3 · tsoc / openmm

10 Jan, 2014 2 commits
- Merge pull request #281 from peastman/master · db9528ca
  peastman authored Jan 10, 2014
```
Updated Developer Guide for 6.0
```
  db9528ca
- Updated Developer Guide for 6.0 · 8c918ca2
  peastman authored Jan 10, 2014
  
  8c918ca2
09 Jan, 2014 6 commits
- Merge pull request #280 from peastman/master · 8e24cfc9
  peastman authored Jan 09, 2014
```
Fixed additional errors on Windows
```
  8e24cfc9
- Bug fix · e14ab7b9
  peastman authored Jan 09, 2014
  
  e14ab7b9
- Fixed additional errors on Windows · 76d592d6
  Peter Eastman authored Jan 09, 2014
  
  76d592d6
- Fixed a bug that could potentially cause LJ energy to be nan · 5c983283
  peastman authored Jan 09, 2014
  
  5c983283
- Merge pull request #279 from peastman/master · d3469b87
  peastman authored Jan 08, 2014
```
Optimizations to CPU GBSA
```
  d3469b87
- Optimizations to CPU GBSA · cf52e69f
  peastman authored Jan 08, 2014
  
  cf52e69f
08 Jan, 2014 2 commits
- Merge pull request #277 from peastman/winvec · 6d356ddc
  peastman authored Jan 08, 2014
```
Fixed lots of compilation errors on Windows
```
  6d356ddc
- Fixed lots of compilation errors on Windows · 72e81e04
  Peter Eastman authored Jan 08, 2014
  
  72e81e04
07 Jan, 2014 7 commits
- Merge pull request #276 from peastman/master · a4f7ac48
  peastman authored Jan 07, 2014
```
Very minor optimization
```
  a4f7ac48
- Very minor optimization · 06db7ac4
  peastman authored Jan 07, 2014
  
  06db7ac4
- Merge pull request #275 from swails/master · 85020137
  peastman authored Jan 06, 2014
```
Fixes salt concentration for GB with a cutoff
```
  85020137
- Merge branch 'master' of https://github.com/swails/openmm · 2cbb8f43
  Jason Swails authored Jan 06, 2014
  
  2cbb8f43
- Merge branch 'master' of https://github.com/SimTk/openmm · 8b44287e
  Jason Swails authored Jan 06, 2014
  
  8b44287e
- Merge pull request #274 from peastman/sfmt · 291484f2
  peastman authored Jan 06, 2014
```
Ensure SFMT data array is correctly aligned
```
  291484f2
- Merge branch 'master' of http://github.com/SimTk/openmm · b3d93583
  Jason Swails authored Jan 06, 2014
  
  b3d93583
06 Jan, 2014 9 commits
- Merge pull request #264 from rmcgibbo/reset-dlopen-flags · 9f957758
  peastman authored Jan 06, 2014
```
Fix weird import segfault with RTLD_GLOBAL
```
  9f957758
- Ensure SFMT data array is correctly aligned · 64b0a6c8
  peastman authored Jan 06, 2014
  
  64b0a6c8
- Merged changes between repositories by hand · 2e83bfc8
  Peter Eastman authored Jan 06, 2014
  
  2e83bfc8
- Improved logic for selecting a platform to better deal with exceptions in context initialization · d91e3f19
  peastman authored Jan 06, 2014
  
  d91e3f19
- Merge pull request #272 from peastman/master · 5e2170ff
  peastman authored Jan 06, 2014
```
Fixed some bugs identified by Valgrind
```
  5e2170ff
- Fixed some bugs identified by Valgrind · fc1d0b5c
  peastman authored Jan 06, 2014
  
  fc1d0b5c
- Merge pull request #271 from peastman/master · 192fe4ca
  peastman authored Jan 06, 2014
```
Workaround for compilation error on some compilers
```
  192fe4ca
- Workaround for compilation error on some compilers · 29bfe077
  peastman authored Jan 06, 2014
  
  29bfe077
- Merge pull request #270 from peastman/host · 742ab844
  peastman authored Jan 06, 2014
```
Added option for setting CUDA host compiler
```
  742ab844
05 Jan, 2014 1 commit
- Merge pull request #268 from jchodera/minor-context-fixes · d3734248
  peastman authored Jan 04, 2014
```
Added missing required kernel names to check of platform capabilities.
```
  d3734248
04 Jan, 2014 1 commit

Added missing required kernel names (ApplyConstraintsKernel and... · 9bb2259d

John Chodera authored Jan 04, 2014

Added missing required kernel names (ApplyConstraintsKernel and VirtualSitesKernel) to check for platform capabilities, since these kernels are initialized in the next code block.

9bb2259d

01 Jan, 2014 1 commit
- Fix misplacement of "kappa" in cutoff-GB expression. · 25580770
  Jason Swails authored Jan 01, 2014
  
  25580770
31 Dec, 2013 3 commits
- Just remove the whole nonsense · 98ffd5fe
  Robert McGibbon authored Dec 30, 2013
  
  98ffd5fe
- unused variables · d5115033
  Robert McGibbon authored Dec 30, 2013
  
  d5115033
- Reset the dlopen flags · bb628e2e
  Robert McGibbon authored Dec 30, 2013
  
  bb628e2e
28 Dec, 2013 1 commit
- Correct treatment of kappa when kappa == 0 and when there is a cutoff. · 2410cbef
  Jason Swails authored Dec 27, 2013
  
  2410cbef
27 Dec, 2013 1 commit

Merge pull request #260 from swails/master · a99915ba

peastman authored Dec 27, 2013

Add GBn2 to the simtk.openmm.app namespace and correct unit handling of implicitSolventKappa

a99915ba

25 Dec, 2013 2 commits

Apparently 1/u.nanometers is a quantity rather than a unit, so the command: · 4c24a43e

Jason Swails authored Dec 25, 2013

implicitSolventKappa = implicitSolventKappa.value_in_unit(1/units.nanometers)

will always fail. The only solution I've found is to take the unit of the
quantity. i.e.:

implicitSolventKappa = implicitSolventKappa.value_in_unit((1/units.nanometers).unit)

4c24a43e

Bring GBn2 into the simtk.openmm.app namespace. Also remove some redundant · ce46b9b0
Jason Swails authored Dec 25, 2013
```
references.
```
ce46b9b0

22 Dec, 2013 4 commits
- Merge pull request #249 from swails/master · 5219d2a5
  peastman authored Dec 22, 2013
```
Add a salt concentration term to the custom GB forces
```
  5219d2a5
- Unit-ify the 0 in implicitSolventKappa. · 38f286e5
  Jason Swails authored Dec 22, 2013
  
  38f286e5
- Oops, 1/length, not length. · 3ca3fe54
  Jason Swails authored Dec 21, 2013
  
  3ca3fe54
- Merge branch 'master' of https://github.com/SimTk/openmm · caefd490
  Jason Swails authored Dec 21, 2013
  
  caefd490