Commits · 77e2ddf49ad3d6fbc5466d702f47151bd735acba · tsoc / openmm

24 Apr, 2013 2 commits
- 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
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
19 Mar, 2013 1 commit
- Throw exception if an atom type is defined twice · bc90b216
  Peter Eastman authored Mar 19, 2013
  
  bc90b216
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
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
22 Oct, 2012 1 commit
- When adding solvent, leave less of a gap around the edge · 967347c4
  Peter Eastman authored Oct 22, 2012
  
  967347c4
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
09 Sep, 2012 1 commit
- Added ACE and NME residues to Amoeba parameter file · 813e8ef6
  Mark Friedrichs authored Sep 09, 2012
  
  813e8ef6
30 Aug, 2012 1 commit
- Bug fix: an argument was being processed incorrectly · 7b6ca364
  Peter Eastman authored Aug 30, 2012
  
  7b6ca364
29 Aug, 2012 1 commit
- Fixed bug where CONECT records were being parsed incorrectly · 84feb016
  Peter Eastman authored Aug 29, 2012
  
  84feb016
28 Aug, 2012 1 commit
- Replaced AmoebaUreyBradleyForce and AmoebaTorsionForce by HarmonicBondForce... · 79e37b50
  Peter Eastman authored Aug 28, 2012
```
Replaced AmoebaUreyBradleyForce and AmoebaTorsionForce by HarmonicBondForce and PeriodicTorsionForce
```
  79e37b50
12 Aug, 2012 1 commit

Lee-Ping's vdw dispersion correction · 5209c1cd

Mark Friedrichs authored Aug 12, 2012

added tests to TestCudaAmoebaVdwForce for dispersion correction using box of 216 water molecules
AmoebaVdwForce and AmoebaMultipoleForce now throw execptions if cutoff > 0.5*(box size)

5209c1cd

19 Jun, 2012 1 commit
- Fixed exception in Modeller.addSolvent() · dfdffc7e
  Peter Eastman authored Jun 19, 2012
  
  dfdffc7e
18 Jun, 2012 1 commit
- Modeller.delete() will delete a chain or residue if all the residues/atoms it contains are deleted · c962c2dd
  Peter Eastman authored Jun 18, 2012
  
  c962c2dd
29 May, 2012 2 commits
- Throw an exception if an XML tag specifies both an atom type and an atom class · 895f8dac
  Peter Eastman authored May 29, 2012
  
  895f8dac
- Cleanup to the GRO file reader · a43e8ece
  Peter Eastman authored May 29, 2012
  
  a43e8ece