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COSMO
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COSMO

Getting started

  • What COSMO does
  • Introduction

Tutorials

  • COSMO Tutorials
    • Tutorial 1 — Single-chain quickstart
    • Tutorial 2 — Models & force fields
    • Tutorial 3 — Periodic box, temperature & pressure
    • Tutorial 4 — Restart & outputs
    • Tutorial 5 — Slab simulation of phase separation (LLPS)
    • Tutorial 6 — Protein–RNA complex
    • Tutorial 7 — Continuous Synthesis through an analytic tunnel (cosmo-cylinder)
    • Tutorial 8 — Continuous Synthesis on a coarse-grained E. coli ribosome (cosmo-csp)

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
      • cosmo.core package
      • cosmo.parameters package
      • cosmo.reporter package
      • cosmo.csp package
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COSMO¶

  • cosmo package
    • Subpackages
      • cosmo.core package
        • Submodules
        • cosmo.core.geometry module
      • cosmo.parameters package
        • Submodules
        • cosmo.parameters.model_parameters module
      • cosmo.reporter package
        • Submodules
        • cosmo.reporter.cosmo_reporter module
      • cosmo.csp package
        • Submodules
        • cosmo.csp.core module
        • cosmo.csp.kinetics module
        • cosmo.csp.protocol module
        • cosmo.csp.cylinder module
        • cosmo.csp.ribosome module
        • cosmo.csp.movie module
        • Module contents
    • Module contents
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