Commits · c4e9dcd22fb8d86889a296a55fec8156fc4681d4 · tsoc / openmm

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16 Apr, 2013 3 commits
- Fixed bugs in reading Gromacs files · c4e9dcd2
  Peter Eastman authored Apr 16, 2013
  
  c4e9dcd2
- Updated version number to 5.1. · 456b8a05
  Peter Eastman authored Apr 16, 2013
  
  456b8a05
- 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
08 Apr, 2013 1 commit
- Added getPeriodicBoxVolume() to State · 9b083022
  Peter Eastman authored Apr 08, 2013
  
  9b083022
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
02 Apr, 2013 1 commit
- GromacsTopFile supports all terms needed for CHARMM force field · 8e995a20
  Peter Eastman authored Apr 02, 2013
  
  8e995a20
29 Mar, 2013 1 commit
- GromacsTopFile processes [pairs] lines correctly · fb13fc68
  Peter Eastman authored Mar 29, 2013
  
  fb13fc68
27 Mar, 2013 1 commit
- Fixed bug reading PDB files with multiple locations for some atoms · 00e0bb96
  Peter Eastman authored Mar 27, 2013
  
  00e0bb96
25 Mar, 2013 1 commit

Cleaned up Python API for XmlSerializer. Also ensure that deserialized... · 4f911c7a

Peter Eastman authored Mar 25, 2013

Cleaned up Python API for XmlSerializer.  Also ensure that deserialized objects are returned as the correct class (see bug 1827)

4f911c7a

19 Mar, 2013 1 commit
- Throw exception if an atom type is defined twice · bc90b216
  Peter Eastman authored Mar 19, 2013
  
  bc90b216
20 Feb, 2013 1 commit

Support for serialization of Integrator base class, and two derived classes:... · c0687411

Yutong Zhao authored Feb 20, 2013

Support for serialization of Integrator base class, and two derived classes: LangevinIntegrator and VerletIntegrator. Also added support for python serialization via a single deserializeIntegrator()

c0687411

12 Feb, 2013 1 commit
- Fixed state pickling in the python API. · 60406edd
  Yutong Zhao authored Feb 12, 2013
  
  60406edd
11 Feb, 2013 1 commit
- Fixed deserializeState interface to take in a string (so it is consistent with... · 1486a99d
  Yutong Zhao authored Feb 11, 2013
```
Fixed deserializeState interface to take in a string (so it is consistent with that of deserializeSystem)
```
  1486a99d
05 Feb, 2013 1 commit
- removed unnecessary print statements · 6371f855
  Yutong Zhao authored Feb 05, 2013
  
  6371f855
24 Jan, 2013 1 commit
- Added state serialization and deserialization support for Python · 5d4f86a4
  Yutong Zhao authored Jan 24, 2013
  
  5d4f86a4
19 Jan, 2013 1 commit
- Added GromacsTopFile · 277ab730
  Peter Eastman authored Jan 19, 2013
  
  277ab730
16 Jan, 2013 1 commit
- Regenerated amber10.xml based on files from AMBER 12 · c7d98471
  Peter Eastman authored Jan 16, 2013
  
  c7d98471
10 Jan, 2013 1 commit
- Added missing imports · 9ca5ce7f
  Peter Eastman authored Jan 10, 2013
  
  9ca5ce7f
21 Dec, 2012 1 commit
- Renamed a misnamed method in AmoebaMultipoleForce · 9b6e8314
  Peter Eastman authored Dec 21, 2012
  
  9b6e8314
18 Dec, 2012 1 commit
- Updated Python version number to 5.0. · e6220a01
  Peter Eastman authored Dec 18, 2012
  
  e6220a01
15 Dec, 2012 1 commit
- Improvement to Python documentation generation · 05416ef4
  Peter Eastman authored Dec 15, 2012
  
  05416ef4
14 Dec, 2012 2 commits
- Added an ewaldErrorTolerance option to AmberPrmtopFile · a6bb39a3
  Peter Eastman authored Dec 14, 2012
  
  a6bb39a3
- Minor fixes · 39267487
  Peter Eastman authored Dec 14, 2012
  
  39267487
03 Dec, 2012 1 commit
- If a PDB file specifies elements, use them (see bug 1773) · 471cbbf0
  Peter Eastman authored Dec 03, 2012
  
  471cbbf0
28 Nov, 2012 1 commit
- Fixed bug that caused ForceField to generate an incorrect System if used multiple times · dbccc9dc
  Peter Eastman authored Nov 28, 2012
  
  dbccc9dc
22 Nov, 2012 1 commit
- StateDataReporter allows an alternate value to be specified for the total mass · 38071b45
  Peter Eastman authored Nov 22, 2012
  
  38071b45
21 Nov, 2012 1 commit
- Removed references to free energy plugin · dabb49a7
  Peter Eastman authored Nov 21, 2012
  
  dabb49a7
22 Oct, 2012 1 commit
- When adding solvent, leave less of a gap around the edge · 967347c4
  Peter Eastman authored Oct 22, 2012
  
  967347c4
18 Oct, 2012 1 commit

LPW attempted bugfixes: (1) Changed unit multipliers in... · 68593ba6

Lee-Ping Wang authored Oct 18, 2012

LPW attempted bugfixes: (1) Changed unit multipliers in AmoebaVdwForce::getParticleParameters (2) Sorted vectors in exclusionLists so it agrees with atomExclusions

68593ba6

28 Sep, 2012 2 commits
- Removed the word "harmonic" from lots of places it didn't belong, including class and method names · c6ebf6e2
  Peter Eastman authored Sep 28, 2012
  
  c6ebf6e2
- Bug fixes to amber_file_parser · 7b4f4e79
  Peter Eastman authored Sep 28, 2012
  
  7b4f4e79
27 Sep, 2012 1 commit
- Major cleanup of the AMOEBA API · 1db349e5
  Peter Eastman authored Sep 27, 2012
  
  1db349e5
20 Sep, 2012 1 commit
- PDBFile loads all frames in the file. Also fixed a bug. · d8545b79
  Peter Eastman authored Sep 20, 2012
  
  d8545b79