Commits · 1f6802f977dc8ec6533153c0366953cbf4a9edfd · tsoc / openmm

"plugins/amoeba/openmmapi/vscode:/vscode.git/clone" did not exist on "f11bafd9c232bab595633eafdbed1331fc86c19f"

10 Nov, 2009 2 commits
- Created OpenCL implementation of CustomBondForce · 1f6802f9
  Peter Eastman authored Nov 10, 2009
  
  1f6802f9
- Created CustomBondForce, along with the reference implementation · 3eb561ad
  Peter Eastman authored Nov 10, 2009
  
  3eb561ad
04 Nov, 2009 1 commit
- Fixed GB/VI test · 1902a137
  Mark Friedrichs authored Nov 04, 2009
  
  1902a137
03 Nov, 2009 2 commits

Mark Friedrichs authored Nov 03, 2009

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail

7a36f461

A few optimizations. Also added a new test case. · 48d93893
Peter Eastman authored Nov 03, 2009

48d93893

28 Oct, 2009 1 commit
- Increased tolerance on test cases that failed intermittently · 986d88af
  Peter Eastman authored Oct 28, 2009
  
  986d88af
23 Oct, 2009 2 commits
- Bug fixes · a5a368d0
  Peter Eastman authored Oct 23, 2009
  
  a5a368d0
- Implemented new method for selecting Ewald and PME parameters · b5eda392
  Peter Eastman authored Oct 23, 2009
  
  b5eda392
13 Oct, 2009 1 commit

Comparison of the forces in the Ewald/PME reference tests is disabled by... · 71d59925

Rossen Apostolov authored Oct 13, 2009

Comparison of the forces in the Ewald/PME reference tests is disabled by default. If set, they are compared to the double precision output from Gromacs.

71d59925

07 Oct, 2009 1 commit
- New test systems for Ewald/PME methods. · 6b0b0a26
  Rossen Apostolov authored Oct 07, 2009
  
  6b0b0a26
04 Oct, 2009 1 commit
- Updated the Ewald/PME tests. · d95e723d
  Rossen Apostolov authored Oct 04, 2009
  
  d95e723d
30 Sep, 2009 1 commit
- Bug fixes and simplifications to integration · 4c489434
  Peter Eastman authored Sep 30, 2009
  
  4c489434
21 Sep, 2009 3 commits
- Fixed a typo in Madelung energy formula. · 21d67074
  Rossen Apostolov authored Sep 21, 2009
  
  21d67074
- Ewald method potential is now compared to the exact value of the Madelung energy. · fd64ac97
  Rossen Apostolov authored Sep 21, 2009
  
  fd64ac97
- New tests for Ewald and PME on both Reference and Cuda platforms. · 68ef42c0
  Rossen Apostolov authored Sep 21, 2009
  
  68ef42c0
12 Sep, 2009 1 commit
- Periodic box size is specified by System rather than NonbondedForce · 15811b7c
  Peter Eastman authored Sep 12, 2009
  
  15811b7c
20 Aug, 2009 1 commit
- Implemented tabulated functions in reference platform · 8f0e6d3c
  Peter Eastman authored Aug 20, 2009
  
  8f0e6d3c
17 Aug, 2009 1 commit
- Changes to fix compilation errors under Windows · 49aa594d
  Peter Eastman authored Aug 17, 2009
  
  49aa594d
12 Aug, 2009 1 commit
- Added Ewald test (same as Cuda version) · 4e141906
  Mark Friedrichs authored Aug 12, 2009
  
  4e141906
03 Aug, 2009 1 commit
- Global parameters defined by CustomNonbondedForce can have default values · d099819a
  Peter Eastman authored Aug 03, 2009
  
  d099819a
30 Jul, 2009 1 commit
- CustomNonbondedForce supports named parameters, global parameters, more flexible combining rules · dad22074
  Peter Eastman authored Jul 30, 2009
  
  dad22074
29 Jul, 2009 1 commit
- Created CustomNonbondedForce, including reference implementation. · a63645c0
  Peter Eastman authored Jul 29, 2009
  
  a63645c0
17 Jul, 2009 1 commit
- Combined the Ewald and PME routines into a single one and added calculation of vdW interactions. · 68e02e80
  Rossen Apostolov authored Jul 17, 2009
  
  68e02e80
14 Jul, 2009 2 commits
- Renamed OpenMMContext to Context · a4020466
  Peter Eastman authored Jul 14, 2009
  
  a4020466
- Allow the user to specify the reaction field dielectric constant · 95b8dbd6
  Peter Eastman authored Jul 14, 2009
  
  95b8dbd6
10 Jul, 2009 1 commit
- Created VariableLangevinIntegrator · 952cfb5f
  Peter Eastman authored Jul 10, 2009
  
  952cfb5f
08 Jul, 2009 1 commit
- Implemented VariableVerletIntegrator::stepTo() · 3adfe31f
  Peter Eastman authored Jul 08, 2009
  
  3adfe31f
07 Jul, 2009 1 commit
- Implemented the PME method in the reference platform. · c66dd5a3
  Rossen Apostolov authored Jul 07, 2009
  
  c66dd5a3
02 Jul, 2009 1 commit
- Automatically select Ewald parameters based on error tolerance · 83d57922
  Peter Eastman authored Jul 02, 2009
  
  83d57922
25 Jun, 2009 1 commit
- Improved algorithm for VariableVerletIntegrator · 9cad8b27
  Peter Eastman authored Jun 25, 2009
  
  9cad8b27
23 Jun, 2009 1 commit
- Created VariableVerletIntegrator · 09786e4b
  Peter Eastman authored Jun 23, 2009
  
  09786e4b
06 May, 2009 1 commit
- Fixed a bug in random number generation for the CUDA platform. Updated test cases. · 852bfaea
  Peter Eastman authored May 06, 2009
  
  852bfaea
01 May, 2009 2 commits
- A test case accidentally got commented got. · ddceaa1b
  Peter Eastman authored May 01, 2009
  
  ddceaa1b
- Created reference implementation of rigid shake algorithm. Added the JAMA package to OpenMM. · 52a68c81
  Peter Eastman authored May 01, 2009
  
  52a68c81
21 Apr, 2009 1 commit
- Moved header files into an openmm subdirectory · 644cc275
  Peter Eastman authored Apr 21, 2009
  
  644cc275
17 Apr, 2009 2 commits
- Modified the API for lots of classes so that the number of... · 64493da6
  Peter Eastman authored Apr 17, 2009
```
Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.
```
  64493da6
- Redesigned the API for specifying exclusions and 1-4 interactions. · 29e3fa57
  Peter Eastman authored Apr 17, 2009
  
  29e3fa57
09 Apr, 2009 1 commit
- Reference code for GB/VI · 297538f7
  Mark Friedrichs authored Apr 09, 2009
  
  297538f7
06 Apr, 2009 1 commit
- Implemented the Ewald summation method in the reference platform. Preliminary... · d3b512ad
  Rossen Apostolov authored Apr 06, 2009
```
Implemented the Ewald summation method in the reference platform. Preliminary cuda prototype is included.
```
  d3b512ad
20 Feb, 2009 1 commit

Implemented setting random seed for reference platform, as well as adding it... · eb0bba22

Peter Eastman authored Feb 20, 2009

Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.

eb0bba22