Steered molecular dynamics is an enhanced sampling method for exploring the force and free energy profiles along a selected direction. Steered MD imitates atomic force microscopy (AFM) experiments and could be very useful to investigate ligand-receptor interactions or unfolding of proteins.
In Steered MD, an additional external force is applied to one or more atoms to keep a constant velocity of motion along a selected coordinate. Restoration of the original free energy profile along this coordinate is theoretically possible from the Jarzynski equality. In practice, however, reconstruction of a reliable energy profile is possible only for a very small force and extensive sampling. Therefore Steered MD is often used together with other methods when binding kinetic parameters are of interest: Steered MD is used to generate unbinding trajectories to define collective variables which are then sampled more extensively with another technique, e.g. umbrella sampling.
1. Izrailev S, Stepaniants S, Balsera M, Oono Y, Schulten K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J. 1997;72: 1568–1581.
For examples of previously performed studies in which Steered molecular dynamics was the primary method used, see the following example cases:
Steered molecular dynamics was also used in the following examples: