COSMO 2026.1

COSMO 2026.1 — the project was renamed to COSMO, RNA gained mpipi support, and a new co-translational protein-synthesis subsystem (cosmo.csp) was added. 87 commits, 324 files, +25,107 / −71,638 since v1.3.1. (Versioning moves to CalVer YEAR.N.)

⚠️ Breaking

• Renamed the project and package hpsOpenMM / hps → COSMO / cosmo. All import paths, class names, console commands, and docs moved from hps* to cosmo*. v1.4 is not import-compatible with v1.3.1.

✨ Added

• cosmo.csp — co-translational protein synthesis subsystem (mirrors topo.csp, on cosmo's sequence-based HPS/mpipi force field — no STRIDE, native contacts, or domain.yaml). Two confinement models:
  • Cylinder model (cosmo-cylinder) — an analytic cylindrical exit tunnel (no ribosome beads; fast, never jams).
  • CG-ribosome model (cosmo-csp) — an explicit coarse-grained ribosome as rigid scenery, with the 3-stage elongation cycle (peptidyl-transfer → translocation → tRNA-binding) and the A→P C-terminus switch. Ribosome structures (borrowed from topo's ribosome-preparation pipeline) are provided for four organisms — E. coli, yeast, N. crassa, and human — swapped via the ribosome key.
• Per-codon kinetics with shipped codon dwell-time tables for E. coli, human, yeast, and N. crassa.
• mRNA generator (cosmo-make-mrna) — synthetic transcripts in fastest, slowest, and median synonymous-codon modes.
• tRNA tether (trna_tether) — per-stage A/P covalent attachment (bond + two orienting angles + improper); prev-N-R backbone tether angle for all IDP models.
• Resume for synthesis runs — continue from the last completed residue (progress.log, consolidated layout; HPC-requeue safe).
• Rigid-bond (AllBonds) support and model-independent CSP steric radii.
• Post-synthesis phases — optional ejection then dissociation free runs.
• Movie tool (cosmo-csp-movie) — stitch per-residue/-stage trajectories into a VMD movie, with --tunnel (analytic tunnel) or --ribosome (CG ribosome) scenery.
• RNA support: CA/P coarse-grained representation (retain the phosphate P bead alongside each Cα); mpipi RNA support (validated).
• New console commands: cosmo-csp, cosmo-cylinder, cosmo-csp-movie, cosmo-make-mrna.
• New utils module; new tutorials 7 (cylinder) and 8 (CG ribosome); new usage pages (continuous/cylinder synthesis, ribosome prep, codon dwell-times, resume, synthesis visualization, consolidated control-options); new logo + favicon.

🔧 Changed

• mpipi uses a 3σ cutoff for every interaction pair.
• Upgraded to OpenMM 8.0 / ParmEd 4.0; prints the OpenMM version and nonbonded cutoff at runtime.
• ISF (intermediate-scattering-function) analysis reimplemented in Julia with curve-fit bounds.
• Cleaner runinfo.log; simulation-control options grouped into ordered categories; tutorials list both console and python -m … forms.

🐛 Fixed

• Convert eps_di from kcal/mol → kJ/mol and document units (#11).
• Fix phosphorylation-residue handling; check residues are consecutive before adding harmonic bonds.
• CSP: tether ½-factor, always-on PTC optimization, retired-key guard.

🗑️ Removed

• Retired cosmo.translation; dropped single-bead ribosome + prep tooling (crop_ribosome, ctf_utils, filter_pdb).

Full changelog: CHANGELOG.md · Compare: v1.3.1...2026.1

Stable version v1.3.1

This version supports for Mpipi model. Currently, all models were tested on Protein, not RNA yet.

Stable version v1.3

Release stable version of hpsOpenMM with new features.
support in this version:

• hps_ss
• parameters for nonbonded potential are moved inside functions, making them are local variable

Full Changelog: 1.2...v1.3

Stable version 1.2

Multi-chains simulation and PBC works.
Parameters for KR scale can recognize Phosphorylation residues

Full Changelog: v1.1...1.2

stable1.1

v1.1

Set for KR is the default model

Stable v1.0

Version 1.0
Ready for production