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