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Analysis Pipeline

All observables computed automatically. Click any to expand method details.

▶ CG-LEVEL OBSERVABLES — collective dynamics — same physics at both levels

Energy

Direct from integrator

PE, KE, total energy. Output: energy_timeseries.png

RMSD / RMSF

Structural drift & fluctuation

Mass-weighted deviation from reference. Output: rmsd.png, rmsf.png

RDF g(r)

Pair correlation

Volume-normalized radial distribution. Output: rdf.png

SASA + Rg

Surface & compactness

Shrake-Rupley SASA + mass-weighted Rg. Output: sasa_rg.png

PMF

Boltzmann inversion

W(r) = −kT ln[P(r)]. Output: pmf.png

Free Energy

2D landscape

F(x,y) = −kT ln[P(x,y)/P_max]. Output: free_energy_landscape_2d.png

AA-level from back-mapped structures

▶ AA-LEVEL OBSERVABLES — requires actual amino acid identity and geometry

H-bonds

Distance < 3.5Å + angle > 120°

Backbone + side-chain. PRO excluded as donor. ARG, LYS, SER, THR, TYR, TRP, ASN, GLN, HIS donors. ASP, GLU, ASN, GLN, HIS, SER, THR, TYR acceptors.

Residue Contacts

Heavy-atom closest approach

Cutoff 4.5Å. CA pre-filter at 12Å. Per amino-acid resolution.

Interface Pairs

Ranked by contact + H-bond

Top 30 pairs with frequency bars. Blue = contact, red = H-bond overlay.

Per-Residue Binding

Hotspot profiles

Sum of contacts per residue. Hotspot residues can be labeled in the output view.

Inter-Chain H-bonds

Backbone N-O network

Angle-validated. Top 20 most persistent pairs.

AA Trajectory

PDB export

Multi-model back-mapped trajectory for Chimera/VMD/PyMOL.

refinement diagnostics

▶ QCLOUD ANALYSIS — specific to the selective-refinement feedback loop

Structural Events

Bond forming/breaking

Classified from correction magnitude spikes above baseline.

Event Timeline

Magnitudes over time

Scatter plot of correction events colored by type.

Energy Decomposition

Per-bead breakdown

Bonded, nonbonded, total per CG bead.

Interaction Energy

Inter-entity LJ

Total LJ interaction between all entity pairs over time.

grouped for multi-chain systems when entity separation is available

▶ BINDING ANALYSIS — automatically detected for multi-chain systems

Entity Detection

Groups by protein type

Same bead count = same protein. Auto-pairs: D-A, E-B, F-C.

Pairwise Energy

LJ binding per pair

Time series of interaction energy between biological binding pairs.

Contact Maps

CG + AA level

Frequency heatmaps at both bead and residue resolution.

Binding Dashboard

4-panel overview

COM distance, contacts, energy, correlation scatter.

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