Simulation dashboard
SARS-CoV-2 Spike glycoprotein · 500 ns production run
Backbone RMSD
1.42 Å
at current frame
Radius of gyration
18.7 Å
compactness
H-bonds
214
intra-protein
Total energy
−4.81e5
kJ/mol
RMSD convergence
Backbone deviation from the starting structure
System energy
Potential energy stabilizing over the trajectory
System composition
As prepared for production
RMSD
Root-mean-square deviation vs. the reference frame
Mean (backbone)
1.31 Å
Max
2.04 Å
Plateau from
~120 ns
Converged
Yes
RMSD over time
Backbone, all-atom, and ligand traces
RMSF
Per-residue fluctuation — flexible loops & termini stand out
Fluctuation per residue
Higher values indicate greater mobility
Radius of gyration
Overall compactness of the fold
Rg over time
A stable Rg suggests the fold is maintained
SASA
Solvent-accessible surface area
SASA over time
Total surface split into hydrophobic and hydrophilic
Hydrogen bonds
Intra-protein H-bond network over time
H-bond count
Number of donor–acceptor pairs per frame
Most occupied pairs
Fraction of frames each bond is present
Contact map
Mean residue–residue distances across the trajectory
Cα–Cα contact matrix
Brighter = closer contact (Å)
0 Å25 Å
Energy
Potential, kinetic and total energy
Energy terms over time
Stable total energy indicates an equilibrated system
Temperature & pressure
Thermostat at 310 K · barostat at 1 bar
Temperature
Target 310 K (NPT ensemble)
Pressure
Target 1 bar
PCA / Essential dynamics
Projection of the trajectory onto its two largest motions
PC1 vs PC2
Each point is a frame, colored by time (blue → cyan)
Eigenvalue scree
Variance captured by each principal component
Free-energy landscape
−kBT ln P(PC1, PC2) — basins are stable states
Energy surface (PC1 × PC2)
Dark blue basins are low-energy conformational states
0 kcal/molhigh
Secondary structure
DSSP-style content over the trajectory
Helix / sheet / coil fraction
Stacked fraction of residues per frame
α-helix
β-sheet
turn / coil
Ramachandran plot
Backbone φ/ψ dihedral distribution
φ vs ψ
Clusters in α-helix and β-sheet regions