Commits · b245e77212179e9cb0060f7f4cff60970519fccf · tsoc / openmm

23 Aug, 2013 1 commit
- Stage python app tests in the build directory · 7e8da785
  Robert McGibbon authored Aug 22, 2013
  
  7e8da785
20 Aug, 2013 1 commit
- force integer division · 6e89e067
  Robert McGibbon authored Aug 19, 2013
  
  6e89e067
19 Aug, 2013 2 commits
- del the context after its call in addHydrogens · f36b8080
  Robert McGibbon authored Aug 19, 2013
  
  f36b8080
- Fixed deserialization error caused by SWIG not setting the object ownership flag (see bug 1902) · b4b121bf
  peastman authored Aug 19, 2013
  
  b4b121bf
15 Aug, 2013 2 commits
- PDBFile was using the wrong data type for its unit cell dimensions · 8f6d3ec1
  peastman authored Aug 15, 2013
  
  8f6d3ec1
- Improvements to Gromacs file processing · 751e7a31
  peastman authored Aug 14, 2013
  
  751e7a31
14 Aug, 2013 1 commit
- simtk.openmm.__version__ always matches the OpenMM version number · 21fc406b
  peastman authored Aug 14, 2013
  
  21fc406b
07 Aug, 2013 1 commit
- Fixed Python API for CustomNonbondedForce.addInteractionGroup() · 5aebb617
  peastman authored Aug 07, 2013
  
  5aebb617
02 Aug, 2013 2 commits
- Get the version number from the CMake script · 54ef6b4c
  peastman authored Aug 02, 2013
  
  54ef6b4c
- Speed optimization to GromacsTopFile · 93055791
  peastman authored Aug 02, 2013
  
  93055791
01 Aug, 2013 3 commits
- Moved Python app layer tests into the main source tree · d1d74008
  peastman authored Aug 01, 2013
  
  d1d74008
- dont want to double quote · 4ed33ef5
  Robert McGibbon authored Aug 01, 2013
  
  4ed33ef5
- create a simtk.openmm.version module that contains the git revision · 509373c6
  Robert McGibbon authored Aug 01, 2013
  
  509373c6
31 Jul, 2013 2 commits
- Handle extra particles correctly when guessing why no template matched a residue. · 16b5edb6
  peastman authored Jul 31, 2013
  
  16b5edb6
- ForceField tries to figure out why no residue matched a template · 9e09ca68
  peastman authored Jul 31, 2013
  
  9e09ca68
27 Jul, 2013 1 commit
- Fix segfault when positions are not 3 dimensional. · 2ad438b7
  Robert McGibbon authored Jul 26, 2013
  
  2ad438b7
26 Jul, 2013 1 commit

Added an argument to addHydrogens() for selecting which Platform to use for... · 187ccbb8

peastman authored Jul 26, 2013

Added an argument to addHydrogens() for selecting which Platform to use for minimization.  Also marked convertWater() as deprecated.

187ccbb8

25 Jul, 2013 1 commit
- Added SWM4-NDP water model · 09efc337
  peastman authored Jul 25, 2013
  
  09efc337
23 Jul, 2013 1 commit
- __all__ should not include symbols that start with _ · 73fdc083
  peastman authored Jul 23, 2013
  
  73fdc083
22 Jul, 2013 3 commits
- add flush instructions · bc9f1c6a
  Robert McGibbon authored Jul 22, 2013
  
  bc9f1c6a
- Add support for pickle protocol 2 for Vec3 · d1334405
  Robert McGibbon authored Jul 21, 2013
  
  d1334405
- return correct subtype for getIntegrator() · 3c1bf2c3
  Robert McGibbon authored Jul 21, 2013
  
  3c1bf2c3
21 Jul, 2013 1 commit
- Changed statedatareporter to not buffer its outstream · cd4b69be
  Robert McGibbon authored Jul 20, 2013
  
  cd4b69be
18 Jul, 2013 1 commit
- Add __repr__ to enums, so that we can print them easily in scripts/python · 9a5ecd8f
  Robert McGibbon authored Jul 17, 2013
  
  9a5ecd8f
13 Jul, 2013 1 commit
- Removed an if statement that was causing addHydrogens() to fail for systems containing OH groups. · 25c22045
  Lee-Ping Wang authored Jul 12, 2013
  
  25c22045
12 Jul, 2013 2 commits
- Removed trailing whitespace · 4941cc7d
  Justin MacCallum authored Jul 12, 2013
  
  4941cc7d
- Fixed ACE and NME groups for modeller. · e1f8c0b3
  Lee-Ping Wang authored Jul 11, 2013
  
  e1f8c0b3
04 Jul, 2013 1 commit
- one more change to the numpy code. last commit was bad · 9349f496
  Robert McGibbon authored Jul 03, 2013
  
  9349f496
03 Jul, 2013 3 commits
- Add an __all__ to openmm.py so that XXX_swigregister functions don't get imported · bd232057
  Robert McGibbon authored Jul 03, 2013
  
  bd232057
- move after the unitstrip · 196d01be
  Robert McGibbon authored Jul 03, 2013
  
  196d01be
- convert numpy arrays to lists in stripUnits · b4607862
  Robert McGibbon authored Jul 03, 2013
  
  b4607862
28 Jun, 2013 1 commit
- Disable reaction field when using implicit solvent (see bug 1881) · b63835e4
  peastman authored Jun 28, 2013
  
  b63835e4
21 Jun, 2013 1 commit
- Revert "Changed gb settings to use strings rather than named constants." · e1a4e015
  Justin MacCallum authored Jun 21, 2013
```
This reverts commit 4572d2e3.
```
  e1a4e015
20 Jun, 2013 2 commits
- Changed gb settings to use strings rather than named constants. · 4572d2e3
  Justin MacCallum authored Jun 20, 2013
  
  4572d2e3
- Fixed Python wrapper for specifying the pressure as a Vec3 · 1e9099cd
  Peter Eastman authored Jun 20, 2013
  
  1e9099cd
13 Jun, 2013 2 commits
- Fixed bugs in addExtraParticles() · 84acc13d
  peastman authored Jun 13, 2013
  
  84acc13d
- Python wrapper for getVirtualSite() returns the correct subclass · ca74ebb8
  peastman authored Jun 13, 2013
  
  ca74ebb8
12 Jun, 2013 2 commits
- change error · b4c52477
  Robert McGibbon authored Jun 12, 2013
  
  b4c52477
- fix negative sign issue, and gracefully degrade precision by lopping off decimal places · 58786bc5
  Robert McGibbon authored Jun 12, 2013
  
  58786bc5
11 Jun, 2013 1 commit
- Avoid writing malformed output when the positions are too large. · 3261df63
  Robert McGibbon authored Jun 11, 2013
  
  3261df63