Commits · 040420761dbfad158e8864f8c0e3f425ff84c436 · tsoc / openmm

03 Aug, 2019 1 commit
- 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 5 commits
- Removed duplicated code. Fixed comment on rounding integers. · 6b6f92a0
  João Rodrigues authored Mar 05, 2019
  
  6b6f92a0
- Make Numpy optional in CustomGBForces · 3111d8cf
  tic20 authored Mar 05, 2019
  
  3111d8cf
- 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
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 3 commits
- Fixed bug in _mbondi_radii() · 0de32856
  tic20 authored Feb 27, 2019
  
  0de32856
- Numpyfication of custom GB forces · 74f6ea57
  tic20 authored Feb 27, 2019
  
  74f6ea57
- Fixed typo in proper dihedral signature · 913410fc
  tic20 authored Feb 27, 2019
  
  913410fc
26 Feb, 2019 4 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
- Optimisation: improper matching in PeriodicTorsionGenerator.createForce · 307b34cb
  tic20 authored Feb 26, 2019
  
  307b34cb
20 Feb, 2019 1 commit
- Leave XML data structure unchanged during parsing. · 0515bdf6
  tic20 authored Feb 20, 2019
  
  0515bdf6
19 Feb, 2019 1 commit
- PDBxFile only closes input file if it opens it. · 5c14022e
  tic20 authored Feb 19, 2019
  
  5c14022e