Commits · 76780eef10fe72a8aadfda0950d699684da28e99 · tsoc / openmm

17 Aug, 2018 1 commit
- Add excetion parameters into NBThole so all nonbonded forces have identical exclusions. · 31f7f355
  huangj authored Aug 17, 2018
  
  31f7f355
14 Aug, 2018 1 commit
- Updated version of CHARMM36 · 5eff3083
  peastman authored Aug 14, 2018
  
  5eff3083
08 Aug, 2018 1 commit
- Fixed stack overflow · 05e816ab
  peastman authored Aug 08, 2018
  
  05e816ab
01 Aug, 2018 1 commit
- Fix an indentation bug, and add a testcase for CHARMM Drude force field. · ba8c16da
  huangj authored Aug 01, 2018
  
  ba8c16da
25 Jul, 2018 1 commit
- fix NameError in getAtomIndexByName · e1c200ba
  Sam Delmerico authored Jul 25, 2018
  
  e1c200ba
23 Jul, 2018 1 commit
- Fixed bug in Python wrapper · f3437eec
  peastman authored Jul 23, 2018
  
  f3437eec
11 Jul, 2018 1 commit
- Finish implementing charmm parser for systems with lonepairs and/or with Drude particles. · 234425d1
  huangj authored Jul 12, 2018
  
  234425d1
10 Jul, 2018 1 commit
- Update the python api for parsing CHARMM par/top/psf files. · 00e88bff
  huangj authored Jul 10, 2018
  
  00e88bff
09 Jul, 2018 1 commit
- Extend CHARMM psf parser to Drude systems. · 7a8c03dd
  Jing Huang authored Jul 09, 2018
  
  7a8c03dd
15 Jun, 2018 1 commit
- Support more features in Gromacs top files · c30fa8e6
  Peter Eastman authored Jun 15, 2018
  
  c30fa8e6
08 Jun, 2018 1 commit
- Fixed problems in adding water with membranes · 52ddcde3
  peastman authored Jun 08, 2018
  
  52ddcde3
22 May, 2018 1 commit
- Handle PDB files with altlocs correctly · d11c2f67
  peastman authored May 22, 2018
  
  d11c2f67
17 May, 2018 1 commit
- Improved speed of applying patches · 79676986
  peastman authored May 17, 2018
  
  79676986
16 May, 2018 1 commit
- Improvements to building membranes · fcee4150
  peastman authored May 16, 2018
  
  fcee4150
15 May, 2018 1 commit
- Improve error checking · 276e8f4d
  peastman authored May 15, 2018
  
  276e8f4d
14 May, 2018 3 commits
- Modeller handles insertion codes · e4e94dbc
  peastman authored May 14, 2018
  
  e4e94dbc
- Better handle empty insertion codes · 46ee62d9
  peastman authored May 14, 2018
  
  46ee62d9
- Preserve PDB insertion codes · 9be26851
  peastman authored May 14, 2018
  
  9be26851
25 Apr, 2018 1 commit
- Improved behavior of adding force field directories · ac27d6b7
  peastman authored Apr 25, 2018
  
  ac27d6b7
24 Apr, 2018 1 commit
- Remove duplicate patches · 39712657
  peastman authored Apr 24, 2018
  
  39712657
16 Apr, 2018 1 commit
- Fixed bug in patch definition · 2ee886a9
  peastman authored Apr 16, 2018
  
  2ee886a9
10 Apr, 2018 1 commit
- Fixed reference to self.force when using a switch function for LJ · b571e82c
  João Rodrigues authored Apr 09, 2018
  
  b571e82c
06 Apr, 2018 1 commit
- CHARMM36 supports disulfide bonds · 80d6bd3b
  peastman authored Apr 06, 2018
  
  80d6bd3b
05 Apr, 2018 2 commits
- Fixed error in determining protein size when building membrane · 6d9bef03
  peastman authored Apr 05, 2018
  
  6d9bef03
- Use g++ instead of clang and fix PythonInstall · ec4344c7
  Jason Swails authored Apr 04, 2018
```
clang is tested everywhere else, and it's not as routinely up-to-date on
my Jenkins machine.

PythonInstall failed on Linux machines where the build/install
directories had paths with spaces in them.
```
  ec4344c7
16 Mar, 2018 1 commit
- Fixed error in SWIG wrapper for CustomIntegrator.addTabulatedFunction() · e193f9d8
  peastman authored Mar 16, 2018
  
  e193f9d8
07 Mar, 2018 2 commits
- use NotImplementedError for raising exception · 6b4d27e9
  Sunhwan Jo authored Mar 07, 2018
  
  6b4d27e9
- provide error description · 2b2c98c0
  Sunhwan Jo authored Mar 06, 2018
  
  2b2c98c0
06 Mar, 2018 1 commit

Sunhwan Jo authored Mar 06, 2018

- Test system is translated to the origin
- Energy is computed again after updating Gromacs input to reflect no-cutoff option (rcoulomb = rlist = rvdw = 0.0)

0db10f6c

04 Mar, 2018 2 commits
- add test case for virtual site/nbfix · 25e253cf
  Sunhwan Jo authored Mar 04, 2018
  
  25e253cf
- make nbfix test to find the term between same atom types · 1d6bfef4
  Sunhwan Jo authored Mar 04, 2018
  
  1d6bfef4
03 Mar, 2018 1 commit
- Regenerated files to fix missing external bonds · d7d3aa20
  peastman authored Mar 03, 2018
  
  d7d3aa20
02 Mar, 2018 1 commit
- Fix disulfides in Amber14 · 715e69e0
  peastman authored Mar 02, 2018
  
  715e69e0
21 Feb, 2018 1 commit
- Added switchDistance option to ForceField.createSystem() · fea6d6f6
  peastman authored Feb 20, 2018
  
  fea6d6f6
19 Feb, 2018 1 commit
- Fixes to impropers · 1fc80007
  peastman authored Feb 19, 2018
  
  1fc80007
15 Feb, 2018 1 commit
- Fixed errors in LJ interactions with CHARMM36 · 71e3bb7a
  peastman authored Feb 15, 2018
  
  71e3bb7a
30 Jan, 2018 1 commit
- Fixes to CHARMM36 force field · 7f067d28
  peastman authored Jan 30, 2018
  
  7f067d28
23 Jan, 2018 1 commit
- Fixed problems related to RMSDForce · 9701ed09
  Peter Eastman authored Jan 23, 2018
  
  9701ed09
18 Jan, 2018 2 commits
- removed default call to condense altogether · 80528f3b
  Alan Grossfield authored Jan 18, 2018
  
  80528f3b
- allow the user to skip parameter condensing · 75b8c17c
  Alan Grossfield authored Jan 18, 2018
  
  75b8c17c