Commits · 117ccbbf74dd79f36742b8b85a55f881e9ac251e · tsoc / openmm

25 Apr, 2017 1 commit
- Created test case for CHARMM impropers fix · 117ccbbf
  peastman authored Apr 25, 2017
  
  117ccbbf
05 Jul, 2016 1 commit
- Eliminated warnings about unclosed files · 258ef062
  peastman authored Jul 05, 2016
  
  258ef062
09 Oct, 2015 1 commit

Add code supporting input with and without units for CharmmPsfFile. · 6b2aa2cc

Jason Swails authored Oct 09, 2015

Add relevant tests (that used to fail). This also fixes a subtle bug where
switching functions were not applied when NBFIXes were specified.

6b2aa2cc

07 Oct, 2015 1 commit
- Test case for charmm permissive read · eb77eb64
  M J Harvey authored Oct 07, 2015
  
  eb77eb64
27 Aug, 2015 1 commit
- Python 2/3 compatibility in single code base, plus python 3 testing on travis. · b7088b74
  peastman authored Aug 10, 2015
  
  b7088b74
22 Apr, 2015 1 commit
- Fix up Residue assignment in CharmmPsfFile Topology · 7f802839
  Jason Swails authored Apr 22, 2015
```
Also fixes the test case.  Everything should pass now.
```
  7f802839
10 Apr, 2015 1 commit

Improve CHARMM parsing when resnums have inscodes · 7b30da6e

Jason Swails authored Apr 10, 2015

Apparently CHARMM PSF files (particularly those printed by VMD's psfgen) can
have an insertion code tacked on to the end of the residue number, meaning that
casting to an integer will invariably fail. We can't just ignore the insertion
code, though, since it will differentiate from the residues that came before and
after (which will likely have the same number -- same general idea as insertion
codes from PDB files). So instead we pull the insertion code off of the residue
number and extend the Residue object to accommodate that.

This is the port of the fix from ParmEd: ParmEd/ParmEd#98

I added a test for this case.

7b30da6e

23 Oct, 2014 1 commit
- Fixed CHARMM parser to work with changes to custom GB models · 5bed3590
  Peter Eastman authored Oct 23, 2014
  
  5bed3590
21 Jul, 2014 1 commit
- Add a test for CHARMM NBFIX and import CharmmPSFWarning into the · d978a87d
  Jason Swails authored Jul 21, 2014
```
simtk.openmm.app namespace to allow users to filter that warning out if they
want to.
```
  d978a87d
15 Apr, 2014 1 commit
- Update the CHARMM API to be consistent with the rest of OpenMM. · 895f9a6f
  Jason Swails authored Apr 14, 2014
  
  895f9a6f
10 Apr, 2014 2 commits

Add support for the Amber GB forces. Put in the correct radii determination · c293c198
Jason Swails authored Apr 10, 2014
```
(again, code pulled from ParmEd) and update the tests to include this.
```
c293c198

Add a couple unittests for CHARMM files. Good thing, too, because they helped · 31f09353

Jason Swails authored Apr 09, 2014

pick up some bugs that were not caught in my initial test following the port
from ParmEd.

All 4 tests pass right now, although no periodic systems are being tested.
Currently CHARMM, XPLOR, and VMD tests are all being run (for the same ala-3
system).

Disable implicit solvent tests, since there is no robust radii assignment
routine yet (the radii are stored in the Amber topology file).  I will port my
assignment routine from ParmEd here shortly and then re-enable the GB tests.

31f09353