GitLab

Improve unit handling in charmm crd file classes.

Fixed a crash with virtual sites in double precision mode

Fix Amber inpcrd file in the examples directory

the 3rd and 4th columns, making it an invalid Amber inpcrd file (which the new
parser cannot handle).

Fixed bug when multiple virtual sites depend on the same particles (see bug 2019)

Make separate lists for dihedrals and the dihedrals with loaded parameters.

Fix the handling and units of box lengths in CHARMM files

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.

Small tweak to fix parsing of par_all36_carb.prm

different from _all_ of the others.

Rewrite Amber inpcrd file parsers

Added TIP3P-FB and TIP4P-FB water models

Fix for static linking

element.

fix the remaining CI issues.

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

Seed default RNG from /dev/urandom

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.