What TOPO does¶

TOPO builds a single one-bead-per-residue, structure-based (Gō-like) model from a folded-protein structure and runs Langevin dynamics on OpenMM. That one model powers two complementary workflows, each with its own set of tutorials:

A. Coarse-grained simulation of folded proteins — take a fully-formed structure and study how it moves, unfolds, and comes apart.
B. Protein synthesis — grow the chain residue by residue on the ribosome and watch it fold as it is made.

Part B builds directly on the Part A model, so start with A if you are new here.

A. Coarse-grained simulation of folded proteins¶

Start from a complete structure and run structure-based MD: folding and unfolding, thermal and mechanical stability, and multidomain motions. Contact energies can be scaled per domain and per interface, so different parts of a protein can be made more or less stable.

Tutorials

1 · Single-domain quickstart — build and run your first simulation of a small single-domain protein, then read its outputs.
2 · Multidomain & per-domain contact scaling — control contact-energy stability within each domain and across interfaces with a domain.yaml.
3 · Restart & outputs — checkpoint and resume a run, and understand every file it writes.
4 · Many independent copies — replicate one protein into many non-interacting copies in a single job.
5 · Optimizing the contact scale (nscale) — automatically calibrate the per-domain and per-interface nscale so every unit stays folded.
6 · Anneal & quench — drive temperature ramps to melt, quench, and observe (un)folding.

Reference

B. Protein synthesis¶

Grow the nascent chain N→C, one residue at a time, so the protein can fold co-translationally as it emerges from the exit tunnel. Both tutorials layer codon-resolved kinetics on the Part A model but differ in how the ribosome exit tunnel is represented — and so in which runner they use: Tutorial 7 uses topo-cylinder (an analytic tunnel), Tutorial 8 uses topo-csp (an explicit coarse-grained ribosome).

Tutorials

7 · Synthesis through an analytic tunnel — the exit tunnel is a cylindrical bore through a wall (no explicit ribosome beads); fast, never jams, and the chain folds co-translationally on egress.
8 · Synthesis on a coarse-grained ribosome — the ribosome-based counterpart: grow the chain through TOPO’s own truncated CG ribosome, then eject the completed protein (worked on 4c5c and P0CX28).

Reference