Title: Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations,
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.