COSMO for IDP simulations

COSMO (COarse-grained Simulation of intrinsically disordered prOteins) is a Python library and command-line toolkit for coarse-grained molecular dynamics of intrinsically disordered proteins (IDPs) and related biomolecules such as RNA and DNA, built on OpenMM. From a sequence, it builds a one-bead-per-residue, sequence-based model and runs Langevin dynamics — interactions come from the sequence, not from a folded structure, so COSMO is built for disordered chains.

The model

• One bead per residue, built directly from the sequence (a CA/P PDB).
• Hydropathy-scale HPS (Ashbaugh–Hatch) or Mpipi (Wang–Frenkel) force field, plus Debye–Hückel electrostatics.
• Additional force fields can be added through the package parameter files.

Workflow A — IDP simulation

• Single-chain dimensions (radius of gyration) from a sequence.
• Periodic box with temperature and pressure coupling.
• Slab simulations of liquid–liquid phase separation (LLPS).
• Protein–RNA complexes and mixtures.
• Checkpoint restart, trajectory output, and final-structure export; CPU/GPU execution.

Workflow B — Protein synthesis

• Grow the nascent chain N→C, one residue at a time, timed by each mRNA codon (O’Brien Continuous Synthesis Protocol).
• cosmo-cylinder — fast analytic cylindrical exit tunnel (no explicit ribosome beads).
• cosmo-csp — growth through an explicit coarse-grained ribosome with codon-timed sub-stages.
• Per-codon dwell-time tables and ribosome preparation.

Code and documentation:

• GitHub repository
• COSMO documentation