Commits · e85b2b7f3879beb805b6b7e1eff546560aed3a46 · tsoc / openmm

05 Jul, 2019 3 commits
- Trying to get appveyor working again · e85b2b7f
  peastman authored Jul 05, 2019
  
  e85b2b7f
- Merge pull request #2340 from peastman/numpy · 686e68dc
  peastman authored Jul 05, 2019
```
Optimized conversion of 1D Numpy array to C++ vector<double>
```
  686e68dc
- Optimized conversion of 1D Numpy array to C++ vector<double> · 71b24fad
  peastman authored Jul 05, 2019
  
  71b24fad
01 Jul, 2019 2 commits
- Merge pull request #2336 from peastman/apoa1 · b9a1bee6
  peastman authored Jul 01, 2019
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Install apoa1.pdb
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  b9a1bee6
- Install apoa1.pdb · 99f8c2c1
  peastman authored Jul 01, 2019
  
  99f8c2c1
28 Jun, 2019 1 commit
- Merge pull request #2332 from peastman/energies · 493a2287
  peastman authored Jun 28, 2019
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Fixed bug in CustomIntegrator
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  493a2287
27 Jun, 2019 1 commit
- Fixed bug in CustomIntegrator · 9695c4cf
  Peter Eastman authored Jun 27, 2019
  
  9695c4cf
24 Jun, 2019 2 commits
- Merge pull request #2328 from peastman/offset · a351c396
  peastman authored Jun 24, 2019
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Fixed error applying parameter offsets with CPU platform
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  a351c396
- Fixed error applying parameter offsets with CPU platform · 35b7189c
  Peter Eastman authored Jun 24, 2019
  
  35b7189c
21 Jun, 2019 2 commits
- Merge pull request #2326 from peastman/ppc · d5905f89
  peastman authored Jun 21, 2019
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Fixed error on PPC
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  d5905f89
- Fixed error on PPC · 204a1dcc
  peastman authored Jun 21, 2019
  
  204a1dcc
16 Jun, 2019 3 commits
- Merge pull request #2317 from jing-huang/master · 6e073b48
  peastman authored Jun 16, 2019
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Support CHARMM psf that contains colinear type of lonepair.
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  6e073b48
- Correct the way to compare vector and to do assertAlmostEqual rather than assertEqual. · 75bedabe
  huangj authored Jun 16, 2019
  
  75bedabe
- Specify the .rtf files to be copied from source to staging area. · 3d04a92e
  Jing Huang authored Jun 16, 2019
  
  3d04a92e
15 Jun, 2019 2 commits
- Merge pull request #2322 from peastman/cv · 325fead1
  peastman authored Jun 15, 2019
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CustomCVForce applies ForceInfos from inner context to the outer one
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  325fead1
- Add a test case for the colinear lonepair facility in CHARMM psf parser. · 95711b88
  huangj authored Jun 16, 2019
  
  95711b88
14 Jun, 2019 2 commits
- CustomCVForce applies ForceInfos from inner context to the outer one · ab92c8ed
  Peter Eastman authored Jun 14, 2019
  
  ab92c8ed
- Update the cgenff parameters files in tests/systems from version 3.1 to 4.1 · cbbc7911
  huangj authored Jun 14, 2019
  
  cbbc7911
12 Jun, 2019 1 commit
- Merge pull request #2318 from peastman/exclusions · 0a4867a9
  peastman authored Jun 11, 2019
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Revised how exclusions are computed with PME
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  0a4867a9
11 Jun, 2019 3 commits
- Fixed error on GPUs that don't support 64 bit atomics · de4c9900
  peastman authored Jun 11, 2019
  
  de4c9900
- Fixed race condition · dbbf7c3e
  Peter Eastman authored Jun 11, 2019
  
  dbbf7c3e
- Fixed error with Drude particles · 11dc1eb6
  Peter Eastman authored Jun 11, 2019
  
  11dc1eb6
07 Jun, 2019 1 commit
- Revised how exclusions are computed with PME · da28ce0e
  Peter Eastman authored Jun 07, 2019
  
  da28ce0e
06 Jun, 2019 1 commit
- Support CHARMM psf that contains colinear type of lonepair. · 9924e408
  Jing Huang authored Jun 07, 2019
  
  9924e408
04 Jun, 2019 1 commit
- Merge pull request #2312 from peastman/sqrt · df52ff73
  peastman authored Jun 04, 2019
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Algebraic optimizations
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  df52ff73
03 Jun, 2019 2 commits

Merge pull request #2314 from dprada/dna_amber_names · 5a244b5c
peastman authored Jun 03, 2019
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Adding alternative names of terminal nucleic acids (5' and 3') and atoms H2', H2'', H5' and H5''.
```
5a244b5c

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3).... · a9a7f2cc

Diego Prada authored Jun 03, 2019

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3). Adding alternative names of atoms H2', H2'', H5' and H5'' for nucleic acids.

a9a7f2cc

01 Jun, 2019 1 commit
- Algebraic optimizations · 0bf7b063
  peastman authored Jun 01, 2019
  
  0bf7b063
08 May, 2019 2 commits
- Merge pull request #2307 from peastman/pdbxlabel · e0b3c2bd
  peastman authored May 08, 2019
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PDBxFile is more robust
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  e0b3c2bd
- PDBxFile is more robust · 21cb4f94
  peastman authored May 08, 2019
  
  21cb4f94
30 Apr, 2019 1 commit
- Merge pull request #2305 from peastman/setpos · 25e12f36
  peastman authored Apr 30, 2019
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Optimized setPositions() from Python
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  25e12f36
29 Apr, 2019 1 commit
- Optimized setPositions() from Python · a7bc22fb
  Peter Eastman authored Apr 29, 2019
  
  a7bc22fb
16 Apr, 2019 3 commits
- Merge pull request #2301 from peastman/hippo2 · 9b523076
  peastman authored Apr 16, 2019
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Improvements to HippoNonbondedForce
```
  9b523076
- Fixed error on older Pythons · c60568b2
  Peter Eastman authored Apr 16, 2019
  
  c60568b2
- ForceField supports HippoNonbondedForce · 78d42678
  Peter Eastman authored Apr 16, 2019
  
  78d42678
12 Apr, 2019 4 commits
- Merge pull request #2299 from jchodera/update-version-number · 43f619bc
  peastman authored Apr 12, 2019
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Update version number to 7.4.0 to match nightly conda dev builds
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  43f619bc
- Update version number to 7.4.0 to match nightly conda dev builds · 617f1421
  Chodera authored Apr 12, 2019
  
  617f1421
- Added a separate scale factor for charge transfer · 682da7b2
  Peter Eastman authored Apr 12, 2019
  
  682da7b2
- Minor optimizations to HIPPO · b53c0f10
  Peter Eastman authored Apr 12, 2019
  
  b53c0f10
09 Apr, 2019 1 commit

Created HippoNonbondedForce (#2296) · 1eec1e15

peastman authored Apr 09, 2019

* Created API for HIPPO force field

* Beginning of reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Completed reference of HIPPO with no cutoff

* Beginning cutoffs/PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Completed reference implementation of HIPPO

* Cleanup and optimization to HIPPO reference

* Further cleanup to HIPPO

* Combined direct space interactions into a single loop

* Compute direct space interactions in quasi-internal frame

* Beginning of CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Finished CUDA implementation of HIPPO

* More features and test cases for HippoNonbondedForce

* Serialization and Python API for HippoNonbondedForce

* Fixed sign error in computing forces

1eec1e15