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Principal parameters for Markov state model analysis using TRAM
| Parameter | Value |
|---|---|
| Initially selected features | Minimum distance of ligand from each residue, selected ligand dihedrals |
| TICA lag time | 5 ns |
| Number of TICA dimensions | 80 |
| Number of clusters (microstates) | 50 or 100 |
| MSM lag time | 1, 2, or 5 ns |
