Commits · d58cc041374e0a94dabcc127bc46661e3a0cc817 · tsoc / openmm

02 Aug, 2013 1 commit
- Speed optimization to GromacsTopFile · 93055791
  peastman authored Aug 02, 2013
  
  93055791
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
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
22 Jul, 2013 2 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
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
15 Jul, 2013 1 commit
- Personal commit to make modeller easier to use · 41e9a095
  leeping authored Jul 15, 2013
  
  41e9a095
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
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 1 commit
- Changed gb settings to use strings rather than named constants. · 4572d2e3
  Justin MacCallum authored Jun 20, 2013
  
  4572d2e3
13 Jun, 2013 1 commit
- Fixed bugs in addExtraParticles() · 84acc13d
  peastman authored Jun 13, 2013
  
  84acc13d
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
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
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
01 May, 2013 1 commit
- Fixed vdw parameters for TIP4P-Ew · 33589ed3
  Peter Eastman authored May 01, 2013
  
  33589ed3
24 Apr, 2013 3 commits
- Improved documentation for loadBondDefinitions() · b2ac07ad
  Peter Eastman authored Apr 24, 2013
  
  b2ac07ad
- Allow GBSA definitions to be split between multiple files · 77e2ddf4
  Peter Eastman authored Apr 24, 2013
  
  77e2ddf4
- Changes to read more PDB files with nucleic acids correctly · aa4dad89
  Peter Eastman authored Apr 24, 2013
  
  aa4dad89
17 Apr, 2013 1 commit
- Bug fixes · e4b38cce
  Peter Eastman authored Apr 17, 2013
  
  e4b38cce
16 Apr, 2013 2 commits
- Fixed bugs in reading Gromacs files · c4e9dcd2
  Peter Eastman authored Apr 16, 2013
  
  c4e9dcd2
- Fixed bug that caused some TOP files to fail · 681f601b
  Peter Eastman authored Apr 16, 2013
  
  681f601b
10 Apr, 2013 1 commit
- Added some PDB residue and atom synonyms used by Tinker · 63955548
  Peter Eastman authored Apr 10, 2013
  
  63955548
03 Apr, 2013 7 commits
- Bug fix · fea6769a
  Peter Eastman authored Apr 03, 2013
  
  fea6769a
- Replaced hydrogenDefinitions argument with a loadHydrogenDefinitions() method · c4e08591
  Peter Eastman authored Apr 03, 2013
  
  c4e08591
- Added Topology.loadBondDefinitions() · a700032d
  Peter Eastman authored Apr 03, 2013
  
  a700032d
- Modeller.addHydrogens() allows the user to provide an XML file with additional residue definitions · cd68d924
  Peter Eastman authored Apr 03, 2013
  
  cd68d924
- Modeller.addHydrogens() returns a list of what variants were used · 47b2ac75
  Peter Eastman authored Apr 03, 2013
  
  47b2ac75
- Improved "no template found" error message to suggest possible causes. · a29ebb6f
  Peter Eastman authored Apr 03, 2013
  
  a29ebb6f
- Robert's refactoring of StateDataReporter to let subclasses add new reported values · 886533b9
  Peter Eastman authored Apr 03, 2013
  
  886533b9