KBbox: Methods

Introduction

In selectively scaled molecular dynamics specific terms in the potential energy of the system are scaled to enhance sampling.

The selectively scaled molecular dynamics (selectively scaled MD) method is similar to the smoothed or scaled molecular dynamics method, since both enhance sampling by scaling the system’s potential energy. The main difference is that in selectively scaled MD only specific terms of the potential energy are scaled. Specific interaction energies can be scaled up or down to achieve the desired event.

Example Cases

For examples of previously performed studies in which Selectively Scaled MD was the primary method used, see the following example cases:

Accelerating Rare Dissociative Processes in Biomolecules Using Selectively Scaled MD Simulations.

Selectively Scaled MD was also used in the following examples:

Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics.

Molecular Simulation

Selectively Scaled MD

Introduction

Example Cases