On the enhanced sampling over energy barriers in molecular dynamics simulations

Area of Science:

• Computational chemistry
• Molecular dynamics
• Statistical mechanics

Background:

• Calculating free energies of multidimensional systems is crucial for understanding molecular behavior.
• Efficient sampling of configuration space, especially over energy barriers, remains a challenge in molecular simulations.

Purpose of the Study:

• To present an efficient sampling method for calculating free energies in multidimensional systems.
• To apply the method to investigate slow barrier crossing dynamics in biological molecules.

Main Methods:

• Utilizes a transformed potential energy surface for efficient sampling.
• Enables sampling of both low and high energy regions and accelerates barrier transitions.
• Does not require predefined reaction coordinates, allowing flexible exploration of configuration space.

Main Results:

• Demonstrates efficient sampling of the configuration space within desired energy ranges.
• Successfully applied to study slow barrier crossing processes in a disaccharide and a dipeptide.

Conclusions:

• The developed method provides an efficient approach for free energy calculations.
• It is particularly useful for studying complex dynamics like slow barrier crossings in biomolecular systems.