Molecular Dynamics

Molecular dynamics simulation computes the time-dependent physical motion of every atom within a molecular system — typically a ligand-protein complex,...

Molecular dynamics simulation computes the time-dependent physical motion of every atom within a molecular system — typically a ligand-protein complex, solvated in explicit water molecules — by numerically integrating Newton's equations of motion under a defined force field describing the interatomic forces, generating a trajectory that reveals how the system's structure evolves over a simulated timescale ranging from nanoseconds to microseconds. In structure-based drug design, molecular dynamics serves several complementary purposes: validating the stability of a docking-predicted binding pose over time (a pose that remains stable throughout an extended simulation is considered a more credible binding hypothesis than one that rapidly dissociates), capturing protein flexibility and induced-fit conformational adjustment that static docking cannot address, and providing the trajectory data required for the more rigorous MM-PBSA/MM-GBSA binding energy calculations described above.