Introduction

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. 

 

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. 

 

 

Computational Tools

Steered molecular dynamics can be performed using the following software tools: