Commits · b6e79d4abaf6d6c99aa4300305483eda6af8aadb · tsoc / openmm

"vscode:/vscode.git/clone" did not exist on "24be1d52707bef16343198725dd62f141a92e2d1"

20 Mar, 2019 2 commits
- Merge pull request #2287 from peastman/groups · b6e79d4a
  peastman authored Mar 20, 2019
```
Improved performance of interaction groups on CPU
```
  b6e79d4a
- Improved performance of interaction groups on CPU · b26b74c0
  Peter Eastman authored Mar 19, 2019
  
  b26b74c0
05 Mar, 2019 9 commits
- Merge pull request #2274 from JoaoRodrigues/ion_fix · 7ada5dd0
  peastman authored Mar 05, 2019
```
Improved ion addition to both addSolvent() and addMembrane()
```
  7ada5dd0
- Removed duplicated code. Fixed comment on rounding integers. · 6b6f92a0
  João Rodrigues authored Mar 05, 2019
  
  6b6f92a0
- Merge pull request #2279 from peastman/ccma · 0ee983bc
  peastman authored Mar 05, 2019
```
Optimized building constraint matrix
```
  0ee983bc
- Merge pull request #2278 from peastman/win · cc5ecb7c
  peastman authored Mar 05, 2019
```
Fixed compilation error on Windows
```
  cc5ecb7c
- Optimized building constraint matrix · f24a84f8
  peastman authored Mar 05, 2019
  
  f24a84f8
- Fixed compilation error on Windows · 93e232df
  peastman authored Mar 05, 2019
  
  93e232df
- Fix squaring of units. Ensure addSolvent passes the right data structure to addIons · 8c8dbed1
  João Rodrigues authored Mar 04, 2019
  
  8c8dbed1
- Ensure coords are always in the proper units and not converted to floats · b9936fb9
  João Rodrigues authored Mar 04, 2019
  
  b9936fb9
- Ensure we only get keys of the dictionary · b0b7548a
  João Rodrigues authored Mar 04, 2019
  
  b0b7548a
02 Mar, 2019 1 commit
- Merge pull request #2269 from tristanic/master · 8ce5a685
  peastman authored Mar 01, 2019
```
Avoid repeated matching of duplicate impropers
```
  8ce5a685
01 Mar, 2019 1 commit
- Implemented private _addIons method that improves placement of ions in... · ec1c8ebe
  João Rodrigues authored Mar 01, 2019
```
Implemented private _addIons method that improves placement of ions in solvated box, specially for membrane systems
```
  ec1c8ebe
27 Feb, 2019 1 commit
- Fixed typo in proper dihedral signature · 913410fc
  tic20 authored Feb 27, 2019
  
  913410fc
26 Feb, 2019 5 commits
- Removed incorrect improper signature code · 10320b39
  tic20 authored Feb 26, 2019
  
  10320b39
- Corrected behaviour of improper caching. · cebb9934
  tic20 authored Feb 26, 2019
  
  cebb9934
- Also cache proper torsion search. · f9540d88
  tic20 authored Feb 26, 2019
```
Has a much smaller effect compared to caching the improper search, but non-negligible and easy to do.
```
  f9540d88
- Merge branch 'master' of github.com:tristanic/openmm · c3e361d2
  tic20 authored Feb 26, 2019
  
  c3e361d2
- Optimisation: improper matching in PeriodicTorsionGenerator.createForce · 307b34cb
  tic20 authored Feb 26, 2019
  
  307b34cb
22 Feb, 2019 2 commits
- Merge pull request #2266 from peastman/vector · dd4eed16
  peastman authored Feb 22, 2019
```
Fixed bug in vector operations in CustomIntegrator on CUDA
```
  dd4eed16
- Fixed bug in vector operations in CustomIntegrator on CUDA · ddcd2f66
  Peter Eastman authored Feb 22, 2019
  
  ddcd2f66
21 Feb, 2019 1 commit
- Merge pull request #1 from pandegroup/master · e182a5be
  Tristan Croll authored Feb 21, 2019
```
Sync with official repository
```
  e182a5be
20 Feb, 2019 2 commits
- Merge pull request #2263 from tristanic/master · f36f2dba
  peastman authored Feb 20, 2019
```
simple optimization to ForceField class
```
  f36f2dba
- Leave XML data structure unchanged during parsing. · 0515bdf6
  tic20 authored Feb 20, 2019
  
  0515bdf6
19 Feb, 2019 6 commits
- Merge pull request #2264 from tristanic/files · 1586d560
  peastman authored Feb 19, 2019
```
Ensuring opened files are properly closed
```
  1586d560
- PDBxFile only closes input file if it opens it. · 5c14022e
  tic20 authored Feb 19, 2019
  
  5c14022e
- Revert "Ensuring opened files are closed properly when done" · 174b57e4
  tic20 authored Feb 19, 2019
```
This reverts commit 5ef91d22.
```
  174b57e4
- Ensuring opened files are properly closed · a52611a8
  tic20 authored Feb 19, 2019
  
  a52611a8
- Ensuring opened files are closed properly when done · 5ef91d22
  tic20 authored Feb 19, 2019
  
  5ef91d22
- out-by-one error in ForceField._TemplateData.addAtom() · 0df0f462
  tic20 authored Feb 19, 2019
  
  0df0f462
18 Feb, 2019 1 commit
- simple optimization to ForceField class · 032c0498
  tic20 authored Feb 18, 2019
  
  032c0498
11 Feb, 2019 2 commits
- Merge pull request #2257 from peastman/selfenergy · bd788d90
  peastman authored Feb 11, 2019
```
Fixed inconsistency in computing Ewald self energy
```
  bd788d90
- Bug fix · 588e5540
  Peter Eastman authored Feb 11, 2019
  
  588e5540
09 Feb, 2019 1 commit
- Fixed inconsistency in computing Ewald self energy · e9a2857a
  Peter Eastman authored Feb 08, 2019
  
  e9a2857a
07 Feb, 2019 1 commit
- Merge pull request #2255 from peastman/minimize · 81bad1bc
  peastman authored Feb 07, 2019
```
Improved behavior of energy minimizer
```
  81bad1bc
06 Feb, 2019 1 commit
- Improved behavior of energy minimizer · a515a27a
  Peter Eastman authored Feb 06, 2019
  
  a515a27a
30 Jan, 2019 1 commit
- Merge pull request #2248 from peastman/customgbtable · a770038f
  peastman authored Jan 30, 2019
```
Fixed error using tabulated functions with a CustomGBForce
```
  a770038f
23 Jan, 2019 2 commits
- Fixed error using tabulated functions with a CustomGBForce · 596be80f
  Peter Eastman authored Jan 23, 2019
  
  596be80f
- Merge pull request #2246 from proteneer/long_double · 30592159
  peastman authored Jan 22, 2019
```
Properly define GBSAOBC alpha beta gamma constants to be doubles.
```
  30592159
22 Jan, 2019 1 commit
- Use regular doubles instead of long double. · 885b63c3
  Yutong Zhao authored Jan 22, 2019
  
  885b63c3