Release v2.11.5

Fixed

• A ring cure relaxed and equilibrated against the wrong topology. Gromacs reads
  the topology from disk; form_rings changes it only in memory and writes nothing.
  close_rings writes one per ladder stage, so after the rings were formed the newest
  file on disk was still the ladder topology --- restraints in place at
  kb = 3e5, and the new C-N bonds not yet present. relax and equilibrate both
  grompp'd against it. Only settle and the ladder itself wrote what they ran.

  Counted on one iteration of 89 rings: ringclose-1-6.top carries 267 type-6
  restraints, exactly 3 per ring, and 11880 bonds; the post-formation ring-1.top has
  0 restraints and 12147 bonds. The command issued was
  grompp -c ringrelax-1-npt.gro -p ringclose-1-6.top --- current coordinates against a
  stale topology, because each mdrun refreshes the coordinate file and nothing refreshed
  the topology.

  So for the whole 100 ps equilibration the rings were held together by restraints
  rather than bonded, with the ladder ending around 0.229 nm against its 0.150 nm
  target, meaning those restraints were still loaded. Successful runs carried a
  Harmonic Pot. term of 2.1e5 kJ/mol throughout. One failure reached 775 K in a 300 K
  stage at -57429 bar with 1809 LINCS warnings, which is that restraint energy coming
  out.

  Every MD stage now writes the topology it is about to run. relax has had this
  defect since the ring cure was introduced, and equilibrate since 2.11.4, so box
  and density traces from any ring-cure build to date are not trustworthy and need
  re-measuring. Conversion, ring counts and the threading filter are unaffected ---
  all are decided before this stage runs.