A MD-based approach designed to increase the conformational space sampled by smoothing the system’s potential energy.
In scaled MD, the potential energy of the solute degrees of freedom is scaled down by an arbitrary factor. In principle, the canonical ensemble can be recovered from a scaled MD simulation, though this is often hindered by a high energetic noise. In applications to protein-ligand dissociation, the protein atoms outside the binding site have to be restrained to prevent protein unfolding.
Smoothed or Scaled Molecular Dynamics (Scaled MD) can be performed using the following software tools:
For examples of previously performed studies in which Smoothed or Scaled Molecular Dynamics (Scaled MD) was the primary method used, see the following example cases:
The folowing tutorial describes the use of Smoothed or Scaled Molecular Dynamics (Scaled MD):