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.
References:
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: