Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations

TL;DR

This paper presents a method to accelerate mean square distance calculations in metadynamics simulations, significantly reducing computational costs and improving scalability for molecular dynamics modeling.

Contribution

The paper introduces an approximation technique that decreases the number of distance calculations in metadynamics, enhancing performance and scalability.

Findings

Achieved substantial speed-up in distance computations.

Validated the method on two molecular systems.

Demonstrated scalability with theoretical and practical analysis.

Abstract

Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing the~simulated process. However, the~evaluation of these variables can include numerous mean square distance calculations that introduce substantial computational demands, thus jeopardize the~benefit of the~approach. Recently, we proposed an~approximative method that significantly reduces the~number of these distance calculations. Here we evaluate the~performance and the~scalability on two molecular systems. We assess the~maximal theoretical speed-up based on the reduction of distance computations and Ahmdal's law and compare it to the~practical speed-up achieved with our implementation.