topo — the stack

four runners · one MD engine · one force field
Control INI control files · one per runner Runners · CLI outer loops · console scripts timing core — no OpenMM Shared MD engine · topo.engine every runner delegates its MD here Synthesis scenery injected into the system · CSP only Model & force field Cα coarse-grain · structure-based Engine backend external Outputs & analysis n_steps n_steps rigid beads · tunnel · A↔P builds Simulation · step() reporters state stitch score Q → adjust nscale → repeat md.ini equilibrium optimize.ini Q targets · nscale csp.ini mRNA · ribosome cylinder.ini tunnel geometry cli · topo-mdrun equilibrium MD build once · quench + production cli · topo-optimize nscale optimizer tune contacts → target Q cli · topo-csp O'Brien synthesis per residue · 3 sub-stages stage1→A · stage2→A · stage3→P cli · topo-cylinder cylinder synthesis analytic tunnel · one segment/res timing · topo.csp.kinetics codon kinetics codon-time tables (mRNA) first-passage-time sampling dwell (s) · scale_factor → steps build_system() CG model · copies · dump PSF setup_simulation() platform · Langevin integrator restart / checkpoint · runinfo step · attach_reporters per-phase DCD / log / chk finalize_simulation() → _final.pdb topo.csp.core · ribosome CSP scenery precompute contacts once · L×L reuse rigid ribosome beads · tunnel wall C-term restraint · A↔P switch topo.core buildCoarseGrainModel() Cα topology · bonds · angles periodic torsions · Yukawa topo.utils.nonbonded build_nonbonded_interaction() structure-based (Go) contacts STRIDE secondary structure Karanicolas–Brooks Rmin/2 radii topo.parameters model_parameters · dihedral per-AA mass · charge · torsions external OpenMM LangevinIntegrator CUDA / CPU platform Simulation.step() Trajectory & state .dcd · .log · .psf _final.pdb · .chk _runinfo.log (provenance) per-length L_<n>/ for synthesis topo-csp-movie stitch → VMD synthesis movie topo.analysis native_contacts Q(t) · fraction native contacts
topo/ · engine.py · core · csp · optimize · analysis

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    node detail

    Every box is clickable. The chips up top light the paths through the stack — Equilibrium, Optimize, Synthesis, Cylinder, Analysis. The one idea: all four runners funnel into one shared MD engine that builds one force-field model and steps it on OpenMM.