Molecular Dynamics Simulation (MD)
MDA computational method that simulates the physical movements of atoms and molecules over time by solving Newton's equations of motion with empirical force fields. MD simulations capture protein flexibility, ligand binding kinetics, conformational changes, and solvent effects at atomic resolution. Simulation timescales range from nanoseconds to milliseconds depending on system size and computational resources.
例
- GROMACS and AMBER — widely used MD simulation packages
- Anton supercomputer achieving millisecond-scale protein simulations
- MD-based binding free energy calculations (MM-GBSA, MM-PBSA)
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A computational method that simulates the physical movements of atoms and molecules over time by solving Newton's equations of motion with empirical force fields. MD simulations capture protein flexibility, ligand …