An example of a MD extension pipeline - see RoyalMD repository for a real workflow ;-)
Pipeline
Step 1: Structure Retrieval
The workflow begins by retrieving crystal structures (e.g., PDB ID: 1IGT) from the Protein Data Bank.
Step 2: Topology & Solvation
We apply force fields and place the molecule in a water box with salt ions.
Step 3: MD Simulation
Molecular Dynamics (MD) calculates the forces on atoms over time. The key feature of IgG is the Hinge Region, allowing the Fab arms to search for antigens.
Step 4: Analysis
Calculate RMSD (Root Mean Square Deviation) and RMSF (Fluctuations) to quantify the flexibility shown in the 3D model here.