Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Acceleration of Mean Square Distance Calculations with Floating Close
  Structure in Metadynamics Simulations   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.

28
The categories of this paper are: alg-geom
37
The categories of this paper are: supr-con
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The categories of this paper are: acc-phys
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The categories of this paper are: hep-th
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The categories of this paper are: solv-int
2
The categories of this paper are: math
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The categories of this paper are: dg-ga
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The categories of this paper are: quant-ph
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The categories of this paper are: comp-gas
4
The categories of this paper are: cond-mat
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The categories of this paper are: nlin
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The categories of this paper are: patt-sol
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The categories of this paper are: math-ph
30
The categories of this paper are: q-alg
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The categories of this paper are: nucl-ex
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The categories of this paper are: cmp-lg