Commits · 48dc97ba6bd0497451377813b78618937a4111ec · tsoc / openmm

08 Oct, 2013 1 commit
- Made identification of plugin directory slightly more robust · d6d7919d
  peastman authored Oct 08, 2013
  
  d6d7919d
02 Oct, 2013 6 commits
- Python records where OpenMM is installed, so it doesn't need to be specified... · a402cf17
  peastman authored Oct 02, 2013
```
Python records where OpenMM is installed, so it doesn't need to be specified with environment variables at runtime
```
  a402cf17
- Fix to PR #152 · 25d8559f
  Robert McGibbon authored Oct 01, 2013
  
  25d8559f
- same fix about list(quantity) vs quantity(list) for unitcell dimensions · 45f31654
  Robert McGibbon authored Oct 01, 2013
  
  45f31654
- typo: extra s · 7cbc52ed
  Robert McGibbon authored Oct 01, 2013
  
  7cbc52ed
- Bugfix: dms.positions should be a Quantity(list(Vec3)), not a list(Quantity(Vec3)) · ee1323b9
  Robert McGibbon authored Oct 01, 2013
  
  ee1323b9
- Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular... · 552544ab
  Robert McGibbon authored Oct 01, 2013
```
Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular import and 1 bugfix where dms wasn't creating the topology correctly when the water was specified in different chains
```
  552544ab
01 Oct, 2013 5 commits
- Add provenance · 25ac85a4
  Robert McGibbon authored Oct 01, 2013
  
  25ac85a4
- Implement virtualsites and better checking of unsupported params/tables · 5a5d8958
  Robert McGibbon authored Oct 01, 2013
  
  5a5d8958
- intermediate commit, work on virtualsites · 303e0fe3
  Robert McGibbon authored Oct 01, 2013
  
  303e0fe3
- reorder the exclusion before the pair_12_6_es_term so simplify code · 2c83421c
  Robert McGibbon authored Oct 01, 2013
  
  2c83421c
- Simpler use of quantity · 8244403c
  Robert McGibbon authored Oct 01, 2013
  
  8244403c
30 Sep, 2013 4 commits
- Add a reader and createSystem interface for Desmond dms files · ecd87763
  Robert McGibbon authored Sep 30, 2013
  
  ecd87763
- Remove the module-level function · 7a44101f
  Robert McGibbon authored Sep 30, 2013
  
  7a44101f
- Move left by one column · 572160e3
  Robert McGibbon authored Sep 30, 2013
  
  572160e3
- add get_by_atomic_number to element · a5e0c8e7
  Robert McGibbon authored Sep 29, 2013
  
  a5e0c8e7
29 Sep, 2013 1 commit
- ATOM lines should be 80 chars · 4ab13768
  Robert McGibbon authored Sep 28, 2013
  
  4ab13768
27 Sep, 2013 2 commits
- Add an elseStack · efd3fedd
  Robert McGibbon authored Sep 26, 2013
  
  efd3fedd
- Fix typo · 4537062c
  Robert McGibbon authored Sep 26, 2013
  
  4537062c
26 Sep, 2013 2 commits
- Fix bug in gromacs top file parser where #else preprocessor directives were not being followed · 0e9144d4
  Robert McGibbon authored Sep 25, 2013
  
  0e9144d4
- Look for gromacs include directory in a more flexible way · 2084a6b0
  Robert McGibbon authored Sep 25, 2013
  
  2084a6b0
17 Sep, 2013 3 commits
- Include a comment at the top of PDB files · 1f4c5c53
  peastman authored Sep 17, 2013
  
  1f4c5c53
- Bug fix to previous commit · bafc4ede
  peastman authored Sep 17, 2013
  
  bafc4ede
- PdbStructure records MODRES records · 61cb61fd
  peastman authored Sep 17, 2013
  
  61cb61fd
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 1 commit
- del the context after its call in addHydrogens · f36b8080
  Robert McGibbon authored Aug 19, 2013
  
  f36b8080