Commits · 8c8256762b036b4541464e55cfc3a44328a5c1b5 · tsoc / openmm

22 Aug, 2019 2 commits

Added W-H combining rule · 7a791b94
Chengwen Liu authored Aug 22, 2019

7a791b94

Improve the performance of sending the AmoebaVdwLambda to Cuda using pinned... · 926e7b9a

Michael Schnieders authored Aug 22, 2019

Improve the performance of sending the AmoebaVdwLambda to Cuda using pinned host memory; Updated the AmoebaVdwForceProxy to version 3, and added backward compatibility to version 2; updated TestAPIUnits.py to handle the per particle lambda flag

926e7b9a

21 Aug, 2019 1 commit
- Force generators that don't use PME still accept it as a nonbonded method · 4b0ac471
  peastman authored Aug 21, 2019
  
  4b0ac471
20 Aug, 2019 1 commit
- set currentStep in DCDReporter · a8846c09
  Andreas Krämer authored Aug 20, 2019
  
  a8846c09
19 Aug, 2019 1 commit

Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods... · 612fc60b

Michael Schnieders authored Aug 19, 2019

Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods exposed in the OpenMM API; implemented the getDefaultParameters() on the AmoebaVdwForceImpl to return 1.0 for AmoebaVdwAlpha; Use AmoebaVdwForce::Lambda() to refer to this parameter rather than the String AmoebaVdwAlpha

612fc60b

12 Aug, 2019 1 commit
- Improved robustness of custom GB forces · c2153753
  peastman authored Aug 12, 2019
  
  c2153753
08 Aug, 2019 1 commit
- Changed forcefield to not use dispersion corrections for CHARMM · b0dacea0
  Andreas Krämer authored Aug 08, 2019
  
  b0dacea0
06 Aug, 2019 5 commits
- Fixed Bondi radius for Cl · 04436ceb
  peastman authored Aug 06, 2019
  
  04436ceb
- Fix whitespace · beb977ae
  Jeff Wagner authored Aug 06, 2019
  
  beb977ae
- Add test that SA energy=0 when gbsaModel is None · 501fcca4
  Jeff Wagner authored Aug 06, 2019
  
  501fcca4
- set SA energy to 0 if GBSAOBCForce is made w SA=None · 74ef3fee
  Jeff Wagner authored Aug 06, 2019
  
  74ef3fee
- fixes for python2 and forcefield class · 1d3804df
  Andreas Krämer authored Aug 06, 2019
  
  1d3804df
05 Aug, 2019 1 commit
- recalculated CHARMM energies for Drude and NBFIX tests · 4c9bb3de
  Andreas Krämer authored Aug 05, 2019
  
  4c9bb3de
03 Aug, 2019 2 commits
- removed old comment · 7719f4aa
  Andreas Krämer authored Aug 03, 2019
  
  7719f4aa
- Throw PSF warning only in serious cases · d59f19e4
  Andreas Krämer authored Aug 02, 2019
```
when the number of molecules does not agree
with the number of holders.
```
  d59f19e4
02 Aug, 2019 2 commits
- added fixes for issue #2353 · f38da875
  Andreas Krämer authored Aug 02, 2019
  
  f38da875
- added broken tests for issue #2353 · 59dfbc18
  Andreas Krämer authored Aug 02, 2019
  
  59dfbc18
01 Aug, 2019 1 commit
- Improved API for setting periodic box vectors in CharmmPsfFile · 202be04d
  peastman authored Aug 01, 2019
  
  202be04d
31 Jul, 2019 1 commit
- Fixed errors with residue insertion codes · 5c8644d8
  peastman authored Jul 31, 2019
  
  5c8644d8
30 Jul, 2019 2 commits
- Fixed error on Windows · 78804789
  peastman authored Jul 30, 2019
  
  78804789
- Fixed error on Python 2.7 · 5e671019
  peastman authored Jul 30, 2019
  
  5e671019
29 Jul, 2019 2 commits
- Made test case more robust · 09cac167
  peastman authored Jul 29, 2019
  
  09cac167
- Removed unnecessary imports that were causing errors · 5274e2d0
  peastman authored Jul 29, 2019
  
  5274e2d0
21 Jul, 2019 1 commit
- Don't parse resid, since we don't do anything with it anyway and it is not... · f3028508
  Jason Swails authored Jul 21, 2019
```
Don't parse resid, since we don't do anything with it anyway and it is not required to be an integer.
```
  f3028508
12 Jul, 2019 2 commits
- Added test case for simulated tempering · 63b78261
  peastman authored Jul 12, 2019
  
  63b78261
- Added simulated tempering and metadynamics classes · e8a72716
  peastman authored Jul 12, 2019
  
  e8a72716
05 Jul, 2019 1 commit
- Optimized conversion of 1D Numpy array to C++ vector<double> · 71b24fad
  peastman authored Jul 05, 2019
  
  71b24fad
16 Jun, 2019 2 commits
- 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 1 commit
- Add a test case for the colinear lonepair facility in CHARMM psf parser. · 95711b88
  huangj authored Jun 16, 2019
  
  95711b88
14 Jun, 2019 1 commit
- Update the cgenff parameters files in tests/systems from version 3.1 to 4.1 · cbbc7911
  huangj authored Jun 14, 2019
  
  cbbc7911
06 Jun, 2019 1 commit
- Support CHARMM psf that contains colinear type of lonepair. · 9924e408
  Jing Huang authored Jun 07, 2019
  
  9924e408
03 Jun, 2019 1 commit

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

08 May, 2019 1 commit
- PDBxFile is more robust · 21cb4f94
  peastman authored May 08, 2019
  
  21cb4f94
29 Apr, 2019 1 commit
- Optimized setPositions() from Python · a7bc22fb
  Peter Eastman authored Apr 29, 2019
  
  a7bc22fb
16 Apr, 2019 2 commits
- Fixed error on older Pythons · c60568b2
  Peter Eastman authored Apr 16, 2019
  
  c60568b2
- ForceField supports HippoNonbondedForce · 78d42678
  Peter Eastman authored Apr 16, 2019
  
  78d42678
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

22 Mar, 2019 1 commit
- Removed spurious "import numpy" line · d2ea8772
  tic20 authored Mar 22, 2019
  
  d2ea8772
05 Mar, 2019 1 commit
- Removed duplicated code. Fixed comment on rounding integers. · 6b6f92a0
  João Rodrigues authored Mar 05, 2019
  
  6b6f92a0