Commits · 698769b901d8be03483320ce929c5895ee992741 · tsoc / openmm

20 Dec, 2020 1 commit

fix Charmm NBThole calculation bug and Improper dihedral parameter match issue (#2952) · 698769b9

qiuzy authored Dec 21, 2020

* nbthole

* Update charmmpsffile.py

* Update charmmpsffile.py

* Update charmmparameterset.py

fix multiple dihedral with the same periodicity and add a warning reminder for improper dihedral

* add test example for NBTHole

add system files of CYT-GUA-CYT DNA segment for testing NBThole

* Update TestCharmmFiles.py

698769b9

18 Aug, 2020 1 commit

Updated to latest values for physical constants (#2802) · b4543a46

peastman authored Aug 18, 2020

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

b4543a46

16 Jul, 2020 1 commit
- Fixed errors · c2a049b0
  Peter Eastman authored Jul 16, 2020
  
  c2a049b0
26 Jun, 2020 1 commit
- Fixed TestMetadynamics · 697ab72e
  Charlles Abreu authored Jun 25, 2020
  
  697ab72e
15 Jun, 2020 1 commit
- Fixed errors in test case · 756b1d91
  peastman authored Jun 15, 2020
  
  756b1d91
11 Jun, 2020 1 commit
- Added 2019 CHARMM polarizable force field · 5c83e423
  peastman authored Jun 11, 2020
  
  5c83e423
04 Jun, 2020 1 commit
- Fixed test case · 68eb50bd
  peastman authored Jun 04, 2020
  
  68eb50bd
28 May, 2020 1 commit
- Made some tests more robust · 44325d07
  peastman authored May 28, 2020
  
  44325d07
22 May, 2020 1 commit
- Created MTSLangevinIntegrator · 2abfbb43
  peastman authored May 22, 2020
  
  2abfbb43
19 Apr, 2020 1 commit
- Allow rounding errors in constrain distance comparison · 53de9f14
  YevChern authored Apr 19, 2020
  
  53de9f14
18 Apr, 2020 1 commit
- Make CharmmPsfFile ignore H-H water bond that is required for rigid water with... · 250e8699
  YevChern authored Apr 18, 2020
```
Make CharmmPsfFile ignore H-H water bond that is required for rigid water with original CHARMM implementation of constrains.
```
  250e8699
31 Mar, 2020 2 commits
- Added drudeMass argument for setting mass of Drude particles · 2ca67c5c
  peastman authored Mar 31, 2020
  
  2ca67c5c
- Patches can define virtual sites · ac6f8942
  peastman authored Mar 31, 2020
  
  ac6f8942
17 Mar, 2020 2 commits
- use assertEqual on sorted list instead of assertCountEqual · d47c51b9
  Zheng Gong authored Mar 17, 2020
  
  d47c51b9
- add test case for constraints and rigidWater in CharmmPsfFile · 91920ef4
  Zheng Gong authored Mar 17, 2020
  
  91920ef4
16 Mar, 2020 1 commit
- bug fix for constraints and rigidWater in CharmmPsfFile · 0c646ace
  Zheng Gong authored Mar 16, 2020
  
  0c646ace
06 Feb, 2020 2 commits
- Replace nonstandard atom and residue names when loading PSF files · a52c30a5
  peastman authored Feb 06, 2020
  
  a52c30a5
- Implemented switchDistance option for GromacsTopFile · 683963b2
  peastman authored Feb 06, 2020
  
  683963b2
17 Jan, 2020 1 commit
- Improved behavior of rigidWater option · 57d85036
  peastman authored Jan 16, 2020
  
  57d85036
06 Jan, 2020 1 commit
- Remove requested lines of ffxml · 5e9ce688
  John Chodera authored Jan 05, 2020
  
  5e9ce688
04 Jan, 2020 3 commits
- Fix typo, and add documentation for 'ordering' · 4f48402f
  John Chodera authored Jan 04, 2020
  
  4f48402f
- Add missing test PDB file · bf57b12e
  John Chodera authored Jan 04, 2020
  
  bf57b12e
- Add a test for 'smirnoff' impropers mode · 12c9af48
  John Chodera authored Jan 04, 2020
  
  12c9af48
30 Dec, 2019 1 commit
- Fixed handling of insertion codes in PDBx/mmCIF files · c16db8e9
  peastman authored Dec 30, 2019
  
  c16db8e9
10 Dec, 2019 1 commit
- Add test for 1-2, 1-3 and 1-4 nonbonded exclusions · 71624456
  Zheng Gong authored Dec 10, 2019
  
  71624456
12 Nov, 2019 1 commit
- runForClockTime() updates currentStep correctly · e275bd08
  peastman authored Nov 12, 2019
  
  e275bd08
05 Nov, 2019 1 commit
- Improved determination of elements from Gromacs top files · 8316b626
  peastman authored Nov 05, 2019
  
  8316b626
01 Nov, 2019 2 commits
- Add python interface tests · 9f46a7fc
  Andy Simmonett authored Nov 01, 2019
  
  9f46a7fc
- Clean up NHC interface and fix bug in swig generator · b3be7aec
  Andy Simmonett authored Nov 01, 2019
  
  b3be7aec
29 Oct, 2019 1 commit
- Minor cleanup based on comments · c6225e7a
  peastman authored Oct 29, 2019
  
  c6225e7a
28 Oct, 2019 1 commit
- Allow multiple matching templates if they assign identical parameters · d88ddb3b
  peastman authored Oct 28, 2019
  
  d88ddb3b
25 Oct, 2019 1 commit
- Added test for addHydrogens to check for atom positions · 46b334ce
  João Rodrigues authored Oct 25, 2019
  
  46b334ce
23 Oct, 2019 1 commit
- Adds test to check ion addition in addMembrane test. Was untested before · 1695878a
  João Rodrigues authored Oct 22, 2019
  
  1695878a
12 Oct, 2019 2 commits
- Forgot to undo my test optimization... · 94d6275b
  joaorodrigues authored Oct 12, 2019
  
  94d6275b
- Modified test_addMembrane to be more thorough and use a realistic system. · 3a09cfe6
  joaorodrigues authored Oct 12, 2019
  
  3a09cfe6
09 Oct, 2019 1 commit
- Added test to check for proper read/write of PDBx/mmCIF files · 25ff85b7
  joaorodrigues authored Oct 09, 2019
  
  25ff85b7
30 Sep, 2019 1 commit
- Add ability to enforce units on input arguments · c1e5ec2f
  peastman authored Sep 30, 2019
  
  c1e5ec2f
19 Sep, 2019 1 commit
- Use correct parameters for nucleic acids with GBn2 · 12fa5430
  peastman authored Sep 19, 2019
  
  12fa5430
05 Sep, 2019 2 commits
- Workaround for limitations of NamedTemporaryFile on Windows · fb3f0677
  peastman authored Sep 05, 2019
  
  fb3f0677
- Support all values of NBXMod in CHARMM parameter files · 0a214970
  peastman authored Sep 05, 2019
  
  0a214970