Commits · abbb36717d9b6f012baa18fced0750f2facc840c · tsoc / openmm

"wrappers/python/vscode:/vscode.git/clone" did not exist on "501fcca4de228aeff8c8f2ae00cefc8f8847f7d5"

15 Mar, 2018 4 commits
- Merge pull request #2019 from peastman/initgroups · abbb3671
  peastman authored Mar 15, 2018
```
Optimized initializing interaction groups
```
  abbb3671
- Optimized initializing interaction groups · e7da5c7b
  peastman authored Mar 15, 2018
  
  e7da5c7b
- Merge pull request #2014 from peastman/groups · c89cbcdb
  peastman authored Mar 14, 2018
```
CustomNonbondedForce with interaction groups uses neighbor lists
```
  c89cbcdb
- Bug fixes · 2df35b4e
  peastman authored Mar 14, 2018
  
  2df35b4e
13 Mar, 2018 5 commits
- Merge pull request #2016 from peastman/nan · c6df2891
  peastman authored Mar 13, 2018
```
Fixed uninitialized memory
```
  c6df2891
- Attempt at fixing compilation error on CPU OpenCL · eb932433
  peastman authored Mar 13, 2018
  
  eb932433
- Fixed uninitialized memory · 98b4d1b7
  peastman authored Mar 13, 2018
  
  98b4d1b7
- Bug fix to switching function when not computing energy · 5cb31cfa
  peastman authored Mar 13, 2018
  
  5cb31cfa
- Optimized finding duplicate interactions in interaction groups · e4653fb7
  peastman authored Mar 13, 2018
  
  e4653fb7
12 Mar, 2018 2 commits
- CustomNonbondedForce with interaction groups uses neighbor list in CUDA · 7639d0bd
  Peter Eastman authored Mar 12, 2018
  
  7639d0bd
- Merge pull request #2013 from pandegroup/7.2_branch · 2305f05f
  peastman authored Mar 12, 2018
```
Merge changes from 7.2.1 into master branch
```
  2305f05f
10 Mar, 2018 1 commit
- CustomNonbondedForce with interaction groups uses neighbor list in OpenCL · fb0cc5e7
  peastman authored Mar 09, 2018
  
  fb0cc5e7
07 Mar, 2018 3 commits
- Merge pull request #2008 from sunhwan/master · 69aa6760
  peastman authored Mar 07, 2018
```
handles virtual_sites2 and nbfix in gromacs topology
```
  69aa6760
- use NotImplementedError for raising exception · 6b4d27e9
  Sunhwan Jo authored Mar 07, 2018
  
  6b4d27e9
- provide error description · 2b2c98c0
  Sunhwan Jo authored Mar 06, 2018
  
  2b2c98c0
06 Mar, 2018 1 commit

Sunhwan Jo authored Mar 06, 2018

- Test system is translated to the origin
- Energy is computed again after updating Gromacs input to reflect no-cutoff option (rcoulomb = rlist = rvdw = 0.0)

0db10f6c

04 Mar, 2018 2 commits
- add test case for virtual site/nbfix · 25e253cf
  Sunhwan Jo authored Mar 04, 2018
  
  25e253cf
- make nbfix test to find the term between same atom types · 1d6bfef4
  Sunhwan Jo authored Mar 04, 2018
  
  1d6bfef4
03 Mar, 2018 4 commits
- Merge pull request #2006 from peastman/version · bbd66275
  peastman authored Mar 03, 2018
```
Updated version number to 7.2.1
```
  bbd66275
- Updated version number to 7.2.1 · 0c9ce3bd
  peastman authored Mar 03, 2018
  
  0c9ce3bd
- Merge pull request #2005 from peastman/ssbond · f49084fc
  peastman authored Mar 03, 2018
```
Regenerated files to fix missing external bonds
```
  f49084fc
- Regenerated files to fix missing external bonds · d7d3aa20
  peastman authored Mar 03, 2018
  
  d7d3aa20
02 Mar, 2018 2 commits
- Merge pull request #2004 from peastman/7.2_branch · 6f169809
  peastman authored Mar 02, 2018
```
Fix disulfides in Amber14
```
  6f169809
- Fix disulfides in Amber14 · 715e69e0
  peastman authored Mar 02, 2018
  
  715e69e0
28 Feb, 2018 1 commit
- Merge pull request #2002 from peastman/7.2_branch · 8bddf3fe
  peastman authored Feb 27, 2018
```
Merge changes from 7.2 branch to main branch
```
  8bddf3fe
21 Feb, 2018 2 commits
- Merge pull request #1998 from peastman/switch · 0f65de7a
  peastman authored Feb 21, 2018
```
Added switchDistance option to ForceField.createSystem()
```
  0f65de7a
- Added switchDistance option to ForceField.createSystem() · fea6d6f6
  peastman authored Feb 20, 2018
  
  fea6d6f6
19 Feb, 2018 2 commits
- Merge pull request #1993 from peastman/7.2_branch · 89d08a94
  peastman authored Feb 19, 2018
```
Fixed errors in LJ interactions with CHARMM36
```
  89d08a94
- Fixes to impropers · 1fc80007
  peastman authored Feb 19, 2018
  
  1fc80007
16 Feb, 2018 2 commits
- Merge pull request #1992 from peastman/arrays · d9756688
  peastman authored Feb 16, 2018
```
Simplification to CudaArray and OpenCLArray
```
  d9756688
- Yet more Windows fixes · c75dba47
  peastman authored Feb 16, 2018
  
  c75dba47
15 Feb, 2018 3 commits
- Another Windows fix · 1082edbc
  peastman authored Feb 15, 2018
  
  1082edbc
- Fixed errors in LJ interactions with CHARMM36 · 71e3bb7a
  peastman authored Feb 15, 2018
  
  71e3bb7a
- Fixed compilation error on Windows · fe339675
  peastman authored Feb 15, 2018
  
  fe339675
14 Feb, 2018 2 commits
- Finished converting CudaArrays. · 372f1724
  Peter Eastman authored Feb 14, 2018
  
  372f1724
- Continuing to convert CudaArrays. · f15f591b
  Peter Eastman authored Feb 14, 2018
  
  f15f591b
13 Feb, 2018 1 commit
- Merge pull request #1990 from mjschnie/master · 979525c7
  peastman authored Feb 13, 2018
```
Fixed an edge case bug for Gyrcuk Radii. 
```
  979525c7
12 Feb, 2018 1 commit
- Began converting CudaArrays. · b8c86406
  Peter Eastman authored Feb 12, 2018
  
  b8c86406
10 Feb, 2018 1 commit

Fixed an edge case bug for Gyrcuk Radii. If the radius (ri) of the atom being... · cf8eea87

Michael Schnieders authored Feb 10, 2018

Fixed an edge case bug for Gyrcuk Radii. If the radius (ri) of the atom being descreened is larger than sum of the separation distance (r) and scaled descreening radius (sk), then there is no descreening. This could happen for carbon atom (ri ~= 2) engulfing its bonded hydrogens (sk < 1).

cf8eea87

09 Feb, 2018 1 commit
- More conversion of OpenCLArrays · b33ee3b0
  peastman authored Feb 08, 2018
  
  b33ee3b0