Commits · 19d92e1d9ea1b878d53658ad4b362c0337fe6a24 · tsoc / openmm

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 2 commits
- Add bonds to Topology based on CONECT records in PDB file · fc71bac8
  Peter Eastman authored Mar 23, 2012
  
  fc71bac8
- Fixed incorrect atom names · b001c4ed
  Peter Eastman authored Mar 23, 2012
  
  b001c4ed
22 Mar, 2012 1 commit
- Fixed capitalization of library name · 6f92b9be
  Peter Eastman authored Mar 22, 2012
  
  6f92b9be
21 Mar, 2012 2 commits
- Generate Python wrapper for RPMDIntegrator · a57facb4
  Peter Eastman authored Mar 21, 2012
  
  a57facb4
- Added option to RPMDIntegrator.getState() to specify force groups · 90007de2
  Peter Eastman authored Mar 21, 2012
  
  90007de2
20 Mar, 2012 4 commits
- DCDReporter writes the current periodic box size rather than the original one · 6f6bee35
  Peter Eastman authored Mar 20, 2012
  
  6f6bee35
- Changes to (maybe?) make CMake not look for Java if you aren't building C and Fortran wrappers · 2304af5d
  Peter Eastman authored Mar 20, 2012
  
  2304af5d
- Implemented serialization of virtual sites · c91f4f2e
  Peter Eastman authored Mar 20, 2012
  
  c91f4f2e
- Tolerate round-off error when checking the box size against the cutoff distance · 56766760
  Peter Eastman authored Mar 20, 2012
  
  56766760
19 Mar, 2012 1 commit

Variable time step integrators correctly report the size of the last step... · 761b4bbf

Peter Eastman authored Mar 19, 2012

Variable time step integrators correctly report the size of the last step taken.  Also improved accuracy of integration unit tests.

761b4bbf

16 Mar, 2012 2 commits
- Made constrained energy minimization hopefully more robust · 420fac9c
  Peter Eastman authored Mar 16, 2012
  
  420fac9c
- NonbondedForce sometimes included energy terms that weren't appropriate to the... · 73b4405a
  Peter Eastman authored Mar 16, 2012
```
NonbondedForce sometimes included energy terms that weren't appropriate to the specified force groups
```
  73b4405a
15 Mar, 2012 3 commits
- Fixed error on some platforms · 064bb5e3
  Peter Eastman authored Mar 15, 2012
  
  064bb5e3
- NonbondedForce sometimes included energy terms that weren't appropriate to the... · 1dffa999
  Peter Eastman authored Mar 15, 2012
```
NonbondedForce sometimes included energy terms that weren't appropriate to the specified force groups
```
  1dffa999
- Python API can specify force groups when requesting a State · ee30f308
  Peter Eastman authored Mar 15, 2012
  
  ee30f308