Commits · 83bc16c88976329f544b0edd5b3c5af46101c15f · tsoc / openmm

20 May, 2012 1 commit
- Added GROMACS coordinate reader and Debye in units. · 83bc16c8
  Lee-Ping Wang authored May 20, 2012
  
  83bc16c8
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
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 1 commit
- 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
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
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
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
22 Feb, 2012 1 commit
- Added missing units for cases when temperature_factor is absent · 6bfe2d8b
  Mark Friedrichs authored Feb 22, 2012
  
  6bfe2d8b
17 Feb, 2012 1 commit
- Modeller supports SPC/E water · 1878512f
  Peter Eastman authored Feb 17, 2012
  
  1878512f
16 Feb, 2012 2 commits
- Support 4 and 5 site water when loading prmtop files · 4412050a
  Peter Eastman authored Feb 16, 2012
  
  4412050a
- Fixed bugs in adding solvent · 663a8db0
  Peter Eastman authored Feb 16, 2012
  
  663a8db0
15 Feb, 2012 1 commit
- 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
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 2 commits
- 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 2 commits
- Deleted file with wrong capitalization · d51a7a5c
  Peter Eastman authored Feb 10, 2012
  
  d51a7a5c
- Implementing addHydrogens() · dfdf8328
  Peter Eastman authored Feb 10, 2012
  
  dfdf8328
08 Feb, 2012 1 commit
- Implemented addSolvent() · 15c272fd
  Peter Eastman authored Feb 08, 2012
  
  15c272fd
02 Feb, 2012 1 commit
- Replaced TIP4P with TIP4P-Ew · b593e034
  Peter Eastman authored Feb 02, 2012
  
  b593e034