SimAtomic Analysis Dashboard

Molecular Dynamics Trajectory Analysis • Generated 2026-01-27 04:14

Simulation Configuration

300.0 K
Temperature
1.0 bar
Pressure
NVT
Ensemble
1,000,000
Total Steps
4.00 ns
Total Time
31,869 atoms
System Size
301.0 ± 1.7 K
Avg Temperature
1260.0 ns/day
Avg Speed
Temperature
i
Potential Energy
i

Structure Overview

Trajectory Animation (25 frames)
i
Loading trajectory...

Job Metadata

Run Details
Workflow Simulation
Protocol Energy Minimization → NVT → Production (4.0 ns)
Force field amber/protein.ff19SB.xml / TIP3P
Reproducibility
OpenMM 8.0
Runner v0.0.1
Worker v0.0.1
Usage
Simulation6m 42s
Simulation Credits7
Analysis26s
Analysis Credits1
Total Runtime7m 9s
Total Credits8
Status ✓ Completed

Key Metrics

200
Total Frames
8
Clusters
72 (36.0%)
Noise Points
1 frames
Correlation Time
-2.319 to 2.475
tIC 1 Range
-3.075 to 3.075
tIC 2 Range
tICA 2D
i
Autocorrelation
i
3D Conformational Space
i

Key Metrics

200
Total Frames
3.33 Å
Avg Protein BB RMSD
4.51 Å
Max Protein BB RMSD
1.45 Å
Avg Ligand RMSD
2.01 Å
Max Ligand RMSD
Stability
i

Key Metrics

Protein Ligand
Interaction Type
200
Total Frames
17.0%
Bound Fraction (<3Å)
3.29 Å
Avg Min Heavy-Atom Dist
11.36 Å
Avg RMSD B w.r.t. A
7.45 Å
Avg COM Distance
10
Avg Contacts
269 Ų
Avg Buried SASA

Group A: protein and backbone

Group B: resname UNL

Interaction Time Series
i
Advanced
Buried SASA
i

Ligand Analysis

Ligand SASA
i
Top Contact Residues
i

Hydrogen Bonds

H-Bond Occupancy by Residue
i
H-Bonds per Frame
i

Salt Bridges

Salt Bridge Occupancy by Residue
i
Salt Bridges per Frame
i
Advanced: Proximity Analysis
Residue Proximity Map
i
Residue Distance Matrix
i
Generated by SimAtomic