Welcome to the COSMO documentation

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 and related biomolecules (RNA/DNA), built on OpenMM. From a sequence it builds a one-bead-per-residue model under the hydropathy-scale HPS (Ashbaugh–Hatch) or mpipi (Wang–Frenkel) force field and runs Langevin dynamics — for single-chain dimensions, liquid–liquid phase separation, protein–RNA complexes, and protein synthesis.

New here? Read What COSMO does to see the two things COSMO does and jump to the right tutorials, and Introduction for installation and package layout.

Getting started

• What COSMO does
• Introduction

Tutorials

• COSMO Tutorials
  • Protein synthesis series (7–8)
  • What is COSMO? (the 1-minute version)
  • How you run it
  • Prerequisites
  • Conventions used in the tutorials

IDP simulation

• Simulation control options

Protein synthesis

• The ribosome structure (get one, or build your own)
• Codon dwell-time tables (per-codon timing)
• Synthesis on a coarse-grained ribosome
• Synthesis through an analytic tunnel (cylinder model)
• Synthesis control options

Python & API reference

• Parameters
• System
• Models
• cosmo.csp package

Full module index

• COSMO
  • cosmo package

Indices and tables

• Index

• Module Index

• Search Page