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, How to install to get it running, and Introduction for the package layout.
Using COSMO in a paper? See How to cite COSMO for how to cite the software and the underlying HPS / Mpipi force fields (and the synthesis references when you run CSP).
Getting started
Tutorials
IDP simulation
Protein synthesis
- Protein synthesis: overview
- The ribosome structure (get one, or build your own)
- Codon dwell-time tables (per-codon timing)
- Synthesis through an analytic tunnel (cylinder model)
- Synthesis on a coarse-grained ribosome
- Resuming long synthesis runs
- Visualizing the synthesis process
- Synthesis control options
Python & API reference
Full module index