Commits · 933f2688dc40074be960330af2110c95f45e7070 · tsoc / openmm

13 Sep, 2013 2 commits
- Added option to increase hydrogen mass · 933f2688
  peastman authored Sep 13, 2013
  
  933f2688
- In rare situations, _matchResidue() would take a very long time to return · edb3759b
  peastman authored Sep 13, 2013
  
  edb3759b
12 Sep, 2013 1 commit
- Fixes to adding hydrogens to RNA · 15d8a466
  peastman authored Sep 11, 2013
  
  15d8a466
11 Sep, 2013 1 commit
- Fixed some errors in definitions of hydrogens · 2f6a06ba
  peastman authored Sep 11, 2013
  
  2f6a06ba
09 Sep, 2013 2 commits
- Fixed compilation errors on some platforms · a1c0f183
  peastman authored Sep 09, 2013
  
  a1c0f183
- Handle exceptions correctly inside getState() · acce09a5
  peastman authored Sep 09, 2013
  
  acce09a5
05 Sep, 2013 1 commit
- PdbStructure records SEQRES records · 5719a05d
  peastman authored Sep 05, 2013
  
  5719a05d
04 Sep, 2013 1 commit
- addHydrogens() does not require a ForceField to be specified · 30b4cf1c
  peastman authored Sep 04, 2013
  
  30b4cf1c
03 Sep, 2013 1 commit
- Minor enhancements/fixes to PDBFile · 808504df
  peastman authored Sep 03, 2013
  
  808504df
29 Aug, 2013 1 commit
- Improved error checking in ForceField · 61ea4d43
  peastman authored Aug 29, 2013
  
  61ea4d43
27 Aug, 2013 2 commits
- Fixed an incorrect sign · f55a30ae
  peastman authored Aug 27, 2013
  
  f55a30ae
- CustomGBForces apply the same energy offset as GBSAOBCForce · 94944787
  peastman authored Aug 26, 2013
  
  94944787
26 Aug, 2013 1 commit
- Fixed bug in Fortran header · cf66c678
  peastman authored Aug 26, 2013
  
  cf66c678
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 2 commits
- simtk.openmm.__version__ always matches the OpenMM version number · 21fc406b
  peastman authored Aug 14, 2013
  
  21fc406b
- Fixed the C and Fortran wrappers, which were broken by the addition of interaction groups · e7233c70
  peastman authored Aug 14, 2013
  
  e7233c70
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 1 commit
- Removed trailing whitespace · 4941cc7d
  Justin MacCallum authored Jul 12, 2013
  
  4941cc7d