Introduction

Targeted MD is an enhanced sampling approach which involves application of a time-dependent, purely geometrical constraint to induce a conformational change to a known target structure.

Targeted molecular dynamics is a powerful approach to generate transition paths in complex biomolecular systems by allowing simulation of more elaborate conformational changes. It is based on a molecular dynamics simulation starting from one conformational state as initial structure and using the other for a directing constraint. 

In Targeted MD, a minimal geometric constraint is introduced which results in an additional constraint force ensuring that the transition towards target structure takes place during the simulation.The transition is enforced independently of the height of energy barriers, while the dynamics of the molecule is only minimally influenced by the constraint.

 

References:

1. Schlitter J, Engels M, Krüger P: Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J Mol Graph 1994, 12:84-89.

Computational Tools

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

Example Cases

For examples of previously performed studies in which Targeted molecular dynamics was the primary method used, see the following example cases: