TRACE Analysis
TRACE (Topological Ring And Cage Enumeration) is a graph-based algorithm for detecting hydrogen-bonded cage structures in clathrate hydrates.How It Works
- H-bond Detection: Identifies hydrogen bonds based on O-O distance (default: 3.5 Å)
- Ring Finding: Enumerates all 5- and 6-membered rings in the H-bond network
- Cage Assembly: Combines rings into complete polyhedral cages
- Classification: Labels cages by their face signature (e.g., 5¹²6²)
Detected Cage Types
| Notation | Name | Structure Type |
|---|---|---|
| 5¹² | Dodecahedron | sI small cage |
| 5¹²6² | Tetrakaidecahedron | sI large cage |
| 5¹²6⁴ | Hexakaidecahedron | sII large cage |
| 5¹²6⁸ | Icosahedron | sH large cage |
Running TRACE
- Upload your
.grofile - Navigate to the ANALYZE tab
- Select TRACE algorithm
- Click RUN TRACE
Terminology
- SEC (Standard Edge-saturated Cage): Complete cage with all H-bonds satisfied
- nSEC (Non-Standard Edge-saturated Cage): Cage with unusual topology
- IC (Incomplete Cage): Partially formed cage structure