Commits · 70ba177d431a7f8fa5039266c0f6035f367e530a · tsoc / openmm

29 May, 2012 2 commits
- Throw an exception if an XML tag specifies both an atom type and an atom class · 895f8dac
  Peter Eastman authored May 29, 2012
  
  895f8dac
- Cleanup to the GRO file reader · a43e8ece
  Peter Eastman authored May 29, 2012
  
  a43e8ece
21 May, 2012 1 commit
- Minor change to work correctly with AMBER restart files · a3db0217
  Peter Eastman authored May 21, 2012
  
  a3db0217
20 May, 2012 1 commit
- Added GROMACS coordinate reader and Debye in units. · 83bc16c8
  Lee-Ping Wang authored May 20, 2012
  
  83bc16c8
11 May, 2012 1 commit
- Checkpointing works with Python · 72f3fe31
  Peter Eastman authored May 11, 2012
  
  72f3fe31
10 May, 2012 1 commit
- Fixed errors building wrappers for CustomCompoundBondForce · 8d2074f5
  Peter Eastman authored May 10, 2012
  
  8d2074f5
07 May, 2012 3 commits
- Implemented Modeller.add() and Modeller.delete() · 36fced55
  Peter Eastman authored May 07, 2012
  
  36fced55
- Bonds were being added to the Topology incorrectly · 12ff40ef
  Peter Eastman authored May 07, 2012
  
  12ff40ef
- Defined a sum() function that works with Quantities. Also fixed a doctest. · c2e05fe8
  Peter Eastman authored May 07, 2012
  
  c2e05fe8
04 May, 2012 1 commit
- Residue indices for atoms were set incorrectly · 0844f4fe
  Peter Eastman authored May 04, 2012
  
  0844f4fe
23 Apr, 2012 3 commits
- Reporters check for NaNs or infinities in output · a4bf2ceb
  Peter Eastman authored Apr 23, 2012
  
  a4bf2ceb
- 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
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
09 Apr, 2012 1 commit
- Tweaked the alignment of the atom name in PDB files · 19d92e1d
  Peter Eastman authored Apr 09, 2012
  
  19d92e1d
04 Apr, 2012 2 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
30 Mar, 2012 2 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
28 Mar, 2012 3 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
- 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 1 commit
- Created StateDataReporter · 724e498b
  Peter Eastman authored Mar 26, 2012
  
  724e498b
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 1 commit
- Generate Python wrapper for RPMDIntegrator · a57facb4
  Peter Eastman authored Mar 21, 2012
  
  a57facb4
20 Mar, 2012 1 commit
- DCDReporter writes the current periodic box size rather than the original one · 6f6bee35
  Peter Eastman authored Mar 20, 2012
  
  6f6bee35
15 Mar, 2012 2 commits
- Fixed error on some platforms · 064bb5e3
  Peter Eastman authored Mar 15, 2012
  
  064bb5e3
- Python API can specify force groups when requesting a State · ee30f308
  Peter Eastman authored Mar 15, 2012
  
  ee30f308
13 Mar, 2012 4 commits
- Avoid writing numbers that are too large to fit in the allowed set of columns · 3eb4fe2e
  Peter Eastman authored Mar 13, 2012
  
  3eb4fe2e
- Apply periodic boundary conditions when reporting coordinates · e59e15b2
  Peter Eastman authored Mar 13, 2012
  
  e59e15b2
- Fixed bug where tuples would sometimes turn into lists when changing their units · da9a3547
  Peter Eastman authored Mar 13, 2012
  
  da9a3547
- Fixed bug where tuples would sometimes turn into lists when changing their units · 63909299
  Peter Eastman authored Mar 13, 2012
  
  63909299
05 Mar, 2012 1 commit
- Improved exception handling: catch any exception, not just OpenMMException · 82159daf
  Peter Eastman authored Mar 05, 2012
  
  82159daf