Commits · b3f88f6fcd000ef3f853e0b6635d78ee6820c016 · tsoc / openmm

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 3 commits
- Replaced TIP4P with TIP4P-Ew · b593e034
  Peter Eastman authored Feb 02, 2012
  
  b593e034
- PdbFile and AmberInpcrdFile can return values as Numpy arrays · e2d8c16e
  Peter Eastman authored Feb 02, 2012
  
  e2d8c16e
- Created Modeller class. Two modeling methods are currently supported:... · deb55264
  Peter Eastman authored Feb 02, 2012
```
Created Modeller class.  Two modeling methods are currently supported: deleteWater() and convertWater()
```
  deb55264
01 Feb, 2012 1 commit
- Use PDB 3.0 nomenclature for the Topology created by AmberPrmtopFile · df60bf0d
  Peter Eastman authored Feb 01, 2012
  
  df60bf0d
26 Jan, 2012 1 commit
- ForceField support TIP4P and TIP5P · 2dd09317
  Peter Eastman authored Jan 26, 2012
  
  2dd09317
23 Jan, 2012 2 commits
- Define both __div__ and __truediv__ to work on all Python versions · bfc1b529
  Peter Eastman authored Jan 23, 2012
  
  bfc1b529
- Changes to support Python 3 · d648613b
  Peter Eastman authored Jan 23, 2012
  
  d648613b
09 Jan, 2012 1 commit
- Made it easier to stop a simulation by pressing control-c · 6c159d06
  Peter Eastman authored Jan 09, 2012
  
  6c159d06
04 Jan, 2012 1 commit
- File was not updated w/ r3053 · fbe20d20
  Mark Friedrichs authored Jan 04, 2012
  
  fbe20d20
03 Jan, 2012 1 commit
- Fixed bug in recognizing incomplete TER records in PDB files · 6c6161cb
  Peter Eastman authored Jan 03, 2012
  
  6c6161cb
28 Nov, 2011 1 commit
- When creating a System, add a CMMotionRemover by default · 9a1b72ff
  Peter Eastman authored Nov 28, 2011
  
  9a1b72ff
24 Nov, 2011 1 commit
- Labute GB/VI parameters · da5196d7
  Mark Friedrichs authored Nov 24, 2011
  
  da5196d7
16 Nov, 2011 4 commits
- Fixed bug in handling wildcards with multiple XML files · 3d670d63
  Peter Eastman authored Nov 16, 2011
  
  3d670d63
- Remove print statement · 60aa3862
  Mark Friedrichs authored Nov 16, 2011
  
  60aa3862
- Remove print statement · 079951ad
  Mark Friedrichs authored Nov 16, 2011
  
  079951ad
- Modify assignment of multipole axis atoms to match Tinker for ambiguous cases · 68318b9b
  Mark Friedrichs authored Nov 16, 2011
```
Use GK overlap factors for Grycuk algorithm (was OBC)
```
  68318b9b
15 Nov, 2011 1 commit
- Name for Coulomb unit was defined incorrectly · f6c08a06
  Peter Eastman authored Nov 15, 2011
  
  f6c08a06