GitLab

(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.

    - existence of velocities and box vectors is auto-detected, so
      loadVelocities and loadBoxVectors are unnecessary
    - recognizes NetCDF-format Amber restart files (which can be written by
      tleap, sander, pmemd, and cpptraj).
    - Restart files coordinate/velocity/box fields have a hard width of 12
      characters and does not ensure that fields are whitespace delimited. This
      commit will correctly parse (valid) Amber restart files in which a
      particular coordinate is <= -100 A or >= 1000 A (not uncommon for restart
      files from sander/pmemd).
    - File format (ASCII vs. NetCDF) is auto-detected.

I deprecated the loadVelocities and loadBoxVectors arguments, since the behavior
does not change (and is correct) whether these variables are set or not. A
DeprecationWarning is emitted if users specify these variables.

the file name (not the path) for "top" and "par" to determine file type.  Often
enough, these files are stored in a "toppar" directory, so all of them will be
interpreted as RTF files.

correction maps in their calculations.