Solution

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Please tell me what kind of model to build

In theory, biomolecular models containing every single atomic detail are the most accurate computational way to probe protein conformational dynamics. In practice, however, due to the expensive computational costs required for simulations with such details, all-atom models are oftentimes applicable only for simulating structural changes on a timescale far shorter than needed for observing biologically relevant events.

PDB File

— or —

Upload your PDB file:

Upload a local PDB file or fetch one by ID from the RCSB Protein Data Bank.

Simulation Settings

Terminal capping option:

Force-field: Box X (nm): Box Y (nm): Box Z (nm): Net charge:

Add salt