Commits · 52c444c579f03523eaf274ccfa03b96fbd009909 · tsoc / openmm

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
04 Jun, 2013 1 commit
- Fixed a bug caused by conflicting definitions of sum() · 7ae8e13a
  peastman authored Jun 04, 2013
  
  7ae8e13a
01 Jun, 2013 3 commits
- Removed duplicate kernels, slightly modified API for Python compatibility. · b7a24d6c
  Lee-Ping authored Jun 01, 2013
  
  b7a24d6c
- Code implemented and passes tests · 665de794
  Lee-Ping authored Jun 01, 2013
  
  665de794
- Created Python API for ring polymer contraction · ffdce362
  peastman authored May 31, 2013
  
  ffdce362
24 May, 2013 1 commit
- Added DrudeSCFIntegrator to the Python wrappers · f8f80693
  peastman authored May 24, 2013
  
  f8f80693
21 May, 2013 1 commit
- ForceField supports DrudeForce · c5ad2202
  peastman authored May 21, 2013
  
  c5ad2202
20 May, 2013 1 commit
- Implemented Modeller.addExtraParticles(). Also some cleanup in ForceField. · 6f98dd5f
  peastman authored May 20, 2013
  
  6f98dd5f
17 May, 2013 1 commit
- Created Python wrapper for Drude plugin · a9f16906
  Peter Eastman authored May 17, 2013
  
  a9f16906
09 May, 2013 1 commit
- Fixed typo in method name · ae847dd7
  Peter Eastman authored May 09, 2013
  
  ae847dd7
08 May, 2013 1 commit
- Removed lots of units code from AMBER file loader, which made it unnecessarily slow · 70ff98db
  Peter Eastman authored May 08, 2013
  
  70ff98db
03 May, 2013 1 commit
- Specified units for some new methods · c4d89122
  Peter Eastman authored May 03, 2013
  
  c4d89122
01 May, 2013 1 commit
- Fixed vdw parameters for TIP4P-Ew · 33589ed3
  Peter Eastman authored May 01, 2013
  
  33589ed3
29 Apr, 2013 1 commit
- Ensure Python interpreter lock gets reacquired when an exception is thrown. · d96606e2
  Peter Eastman authored Apr 29, 2013
  
  d96606e2