Commits · 191bca722a7e59bee1c766562f68d30cd758f551 · tsoc / openmm

25 Apr, 2012 1 commit
- Documentation updates for 4.1. Created new PDFs. · 191bca72
  Peter Eastman authored Apr 25, 2012
  
  191bca72
24 Apr, 2012 1 commit
- Added a StateDataReporter to the Python examples · 7a45cf24
  Peter Eastman authored Apr 24, 2012
  
  7a45cf24
23 Apr, 2012 4 commits
- Reporters check for NaNs or infinities in output · a4bf2ceb
  Peter Eastman authored Apr 23, 2012
  
  a4bf2ceb
- Added tapering function to AMOEBA vdw function; fixed issue w/ zeroing of vdw forces. · 4e480ff6
  Mark Friedrichs authored Apr 23, 2012
  
  4e480ff6
- Set units correctly on Numpy arrays · cb0b20f5
  Peter Eastman authored Apr 23, 2012
  
  cb0b20f5
- Fixed bugs setting up nonbonded and GB forces · c9d7d1e9
  Peter Eastman authored Apr 23, 2012
  
  c9d7d1e9
21 Apr, 2012 1 commit
- Report density in g/mL · ee1ec687
  Peter Eastman authored Apr 21, 2012
  
  ee1ec687
20 Apr, 2012 1 commit
- Mike Garrahan's fix to the Fortran wrapper for getState() · de366ef7
  Peter Eastman authored Apr 20, 2012
  
  de366ef7
15 Apr, 2012 1 commit
- Bug fix for cases where box is not cubic · d407854c
  Mark Friedrichs authored Apr 15, 2012
  
  d407854c
13 Apr, 2012 1 commit
- The wrong path was being used for the OpenMM library · be8774b0
  Peter Eastman authored Apr 13, 2012
  
  be8774b0
12 Apr, 2012 1 commit
- Tolerate errors uninstalling previous versions · b3fe05e9
  Peter Eastman authored Apr 12, 2012
  
  b3fe05e9
11 Apr, 2012 2 commits
- Changed linking instructions to avoid a crash on Linux · 99b0f3bb
  Peter Eastman authored Apr 11, 2012
  
  99b0f3bb
- Minor optimization · f5ccdb60
  Mark Friedrichs authored Apr 11, 2012
  
  f5ccdb60
10 Apr, 2012 1 commit
- Fixed bug in CustomIntegrator computing global parameters · 90a5e2db
  Peter Eastman authored Apr 10, 2012
  
  90a5e2db
09 Apr, 2012 1 commit
- Tweaked the alignment of the atom name in PDB files · 19d92e1d
  Peter Eastman authored Apr 09, 2012
  
  19d92e1d
07 Apr, 2012 1 commit
- Updated version number to 4.1 · bc6e8fa9
  Peter Eastman authored Apr 07, 2012
  
  bc6e8fa9
05 Apr, 2012 4 commits
- Restructured examples directory to better match how it gets installed · baa4dcfd
  Peter Eastman authored Apr 05, 2012
  
  baa4dcfd
- Disable using AMD GPUs on OS X · 50096c2b
  Peter Eastman authored Apr 05, 2012
  
  50096c2b
- Updated documentation to specify CUDA 4.1. Generated new PDFs of manuals. · 4b623f7e
  Peter Eastman authored Apr 05, 2012
  
  4b623f7e
- successive over-relaxation factor changed from 0.70 to 0.55 (latest TINKER valueO · cda5830c
  Mark Friedrichs authored Apr 05, 2012
```
fixed problem w/ storage of PME induced dipoles
```
  cda5830c
04 Apr, 2012 5 commits
- Implement __copy__() and __deepcopy__() for Forces · 681ab7ff
  Peter Eastman authored Apr 04, 2012
  
  681ab7ff
- Bug fix · dea037c3
  Peter Eastman authored Apr 04, 2012
  
  dea037c3
- Updated which example files get installed · 95aa4823
  Peter Eastman authored Apr 04, 2012
  
  95aa4823
- Cleaned up and reorganized docs directory · c56b975b
  Peter Eastman authored Apr 04, 2012
  
  c56b975b
- Excluded a few classes from the Python documentation · c2fdf7fd
  Peter Eastman authored Apr 04, 2012
  
  c2fdf7fd
03 Apr, 2012 1 commit
- Lots of updates to documentation based on changes in 4.1. · 1d043ff5
  Peter Eastman authored Apr 03, 2012
  
  1d043ff5
02 Apr, 2012 1 commit
- Force grid(0,0,0) element to 0 · 084b5c97
  Mark Friedrichs authored Apr 02, 2012
  
  084b5c97
30 Mar, 2012 3 commits
- Lots of improvements to Python API documentation · aab77399
  Peter Eastman authored Mar 30, 2012
  
  aab77399
- Use Doxygen to generate API docs for Python. This involved lots of changes... · cf4c2287
  Peter Eastman authored Mar 30, 2012
```
Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.
```
  cf4c2287
- Sign flipped on energy term · c8764170
  Mark Friedrichs authored Mar 30, 2012
  
  c8764170
28 Mar, 2012 4 commits
- Lots of optimizations to creating systems from prmtop files · b8bf8fbd
  Peter Eastman authored Mar 28, 2012
  
  b8bf8fbd
- All options for StateDataReporter default to False · 689fd4d4
  Peter Eastman authored Mar 28, 2012
  
  689fd4d4
- Reciprocal space force group defaults to "same as direct space force group" · 5b5e2cb6
  Peter Eastman authored Mar 28, 2012
  
  5b5e2cb6
- Allow specifying solute and solvent dielectrics for GBSAOBCForce · 33badc47
  Peter Eastman authored Mar 28, 2012
  
  33badc47
27 Mar, 2012 3 commits
- Added license notice to Python files · b3f88f6f
  Peter Eastman authored Mar 27, 2012
  
  b3f88f6f
- Support <Script> tag in force field files · 5fd130f4
  Peter Eastman authored Mar 27, 2012
  
  5fd130f4
- Added Christoph Klein's implementation of AMBER GB models as custom forces · dce2d427
  Peter Eastman authored Mar 27, 2012
  
  dce2d427
26 Mar, 2012 2 commits
- Created StateDataReporter · 724e498b
  Peter Eastman authored Mar 26, 2012
  
  724e498b
- An attempt at making references between plugins get resolved correctly on OS X · ca9cf05f
  Peter Eastman authored Mar 26, 2012
  
  ca9cf05f
23 Mar, 2012 1 commit
- Add bonds to Topology based on CONECT records in PDB file · fc71bac8
  Peter Eastman authored Mar 23, 2012
  
  fc71bac8