Dynamics (RMSD/RMSF)
Source: src/lib/md/MdDynamicsPanel.svelte, src/lib/md/MdAnalysisPane.svelte
Overview
Computes RMSD (Root Mean Square Deviation) and RMSF (Root Mean Square Fluctuation) from MD trajectories to quantify structural stability and per-atom flexibility.
Components
MdDynamicsPanel
Interactive panel for RMSD/RMSF computation and visualization.
MdAnalysisPane
Parent pane orchestrating all MD analysis tools.
Metrics
RMSD
Measures how much the structure has changed from a reference frame over time.
RMSF
Measures the average fluctuation of each atom around its mean position.
Server API
Endpoint: POST /api/md/rmsd
Parameters
reference_frame— Index of the reference frame (default: 0)atom_selection— Which atoms to includealignment— Whether to align frames before computing