Commits · 68593ba6884b9dd211b76059f08a218d5956c6b0 · tsoc / openmm

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
10 Sep, 2012 1 commit
- Release the Python global interpreter lock during expensive operations · 32d3f86d
  Peter Eastman authored Sep 10, 2012
  
  32d3f86d
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 2 commits
- Changes to work correctly with the latest version of Doxygen · 97470a7d
  Peter Eastman authored Aug 29, 2012
  
  97470a7d
- Fixed bug where CONECT records were being parsed incorrectly · 84feb016
  Peter Eastman authored Aug 29, 2012
  
  84feb016
28 Aug, 2012 3 commits
- Fixed formatting errors in Doxygen comments. · 16e2b1e3
  Peter Eastman authored Aug 28, 2012
  
  16e2b1e3
- Added a getForces() method to System. Also fixed some formatting errors in Doxygen comments. · 71971ba6
  Peter Eastman authored Aug 28, 2012
  
  71971ba6
- 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

20 Jun, 2012 1 commit

Added AmoebaMultipoleForce::getSystemMultipoleMoments() to get system... · 8eb6850d

Mark Friedrichs authored Jun 20, 2012

Added AmoebaMultipoleForce::getSystemMultipoleMoments() to get system multipole moments; based on TINKER subroutine moments()

8eb6850d

19 Jun, 2012 1 commit
- Fixed exception in Modeller.addSolvent() · dfdffc7e
  Peter Eastman authored Jun 19, 2012
  
  dfdffc7e
18 Jun, 2012 2 commits
- 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
- Return dimensionless quantities as numbers, not Quantities with unit=dimensionless. · 15a68e22
  Peter Eastman authored Jun 18, 2012
  
  15a68e22
15 Jun, 2012 1 commit
- Added code to calculate electrostatic potential given vector of grid points · e79b262b
  Mark Friedrichs authored Jun 15, 2012
  
  e79b262b
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
21 May, 2012 1 commit
- Minor change to work correctly with AMBER restart files · a3db0217
  Peter Eastman authored May 21, 2012
  
  a3db0217
20 May, 2012 1 commit
- Added GROMACS coordinate reader and Debye in units. · 83bc16c8
  Lee-Ping Wang authored May 20, 2012
  
  83bc16c8
11 May, 2012 1 commit
- Checkpointing works with Python · 72f3fe31
  Peter Eastman authored May 11, 2012
  
  72f3fe31
10 May, 2012 1 commit
- Fixed errors building wrappers for CustomCompoundBondForce · 8d2074f5
  Peter Eastman authored May 10, 2012
  
  8d2074f5
07 May, 2012 3 commits
- Implemented Modeller.add() and Modeller.delete() · 36fced55
  Peter Eastman authored May 07, 2012
  
  36fced55
- Bonds were being added to the Topology incorrectly · 12ff40ef
  Peter Eastman authored May 07, 2012
  
  12ff40ef
- Defined a sum() function that works with Quantities. Also fixed a doctest. · c2e05fe8
  Peter Eastman authored May 07, 2012
  
  c2e05fe8
04 May, 2012 1 commit
- Residue indices for atoms were set incorrectly · 0844f4fe
  Peter Eastman authored May 04, 2012
  
  0844f4fe
23 Apr, 2012 3 commits
- Reporters check for NaNs or infinities in output · a4bf2ceb
  Peter Eastman authored Apr 23, 2012
  
  a4bf2ceb
- Set units correctly on Numpy arrays · cb0b20f5
  Peter Eastman authored Apr 23, 2012
  
  cb0b20f5
- Fixed bugs setting up nonbonded and GB forces · c9d7d1e9
  Peter Eastman authored Apr 23, 2012
  
  c9d7d1e9
21 Apr, 2012 1 commit
- Report density in g/mL · ee1ec687
  Peter Eastman authored Apr 21, 2012
  
  ee1ec687
13 Apr, 2012 1 commit
- The wrong path was being used for the OpenMM library · be8774b0
  Peter Eastman authored Apr 13, 2012
  
  be8774b0
12 Apr, 2012 1 commit
- Tolerate errors uninstalling previous versions · b3fe05e9
  Peter Eastman authored Apr 12, 2012
  
  b3fe05e9
09 Apr, 2012 1 commit
- Tweaked the alignment of the atom name in PDB files · 19d92e1d
  Peter Eastman authored Apr 09, 2012
  
  19d92e1d
04 Apr, 2012 2 commits
- Implement __copy__() and __deepcopy__() for Forces · 681ab7ff
  Peter Eastman authored Apr 04, 2012
  
  681ab7ff
- Bug fix · dea037c3
  Peter Eastman authored Apr 04, 2012
  
  dea037c3
30 Mar, 2012 2 commits
- Lots of improvements to Python API documentation · aab77399
  Peter Eastman authored Mar 30, 2012
  
  aab77399
- Use Doxygen to generate API docs for Python. This involved lots of changes... · cf4c2287
  Peter Eastman authored Mar 30, 2012
```
Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.
```
  cf4c2287