GitLab

the switchDistance argument to CharmmPsfFile.createSystem().

Also add a check to protect against negative switching distances.

    - Adjust CharmmPsfFile parser to accept multiple blank lines before the
      NATOM record (I saw 1 PSF file like this... not sure how common it really
      is)
    - Removed the shebang line from element.py and removed execute permissions--
      it should never be executed directly (evidenced by the fact that the
      original shebang line was wrong and would never work, anyway).
    - Fix a test to determine if a Bond is part of an Angle in the PSF data
      structures.

(which means that consecutive residues may have the same residue number _and_
name, but are different residues).

former has a single entry for all unique dihedrals. The latter has a separate
entry for every _term_ of every dihedral (and the latter is the one with the
parameters loaded into it). This way, parameter sets can be reloaded at will
without relying on the hack that createSystem previously employed (i.e., backing
up the dihedral array, clobbering it, then putting it back). This way is cleaner
and safer (although functionally equivalent for typical OpenMM use).

boxVectors, so they should be a property computed from the vectors). Also make
sure that any attempts to change the boxVectors correspondingly deletes the
cached copies of the box lengths so they are recomputed if necessary.

different from _all_ of the others.

element.

fix the remaining CI issues.

Also make sure .ncrst files are copied over in the test directory.

and angles makes numbers exactly 0 that _should_ be zero (but aren't due to
precision and round-off issues).

Now the box vector code in the prmtop file is fully general for every type of
box that Amber supports.

Again, this will need to be done in the future anyway for general triclinic
support.