Informace o publikaci

Reducing the number of mean-square deviation calculations with floating close structure in metadynamics

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PAZÚRIKOVÁ Jana KŘENEK Aleš SPIWOK Vojtěch ŠIMKOVÁ Mária

Druh Článek v odborném periodiku
Časopis / Zdroj Journal of Chemical Physics
Fakulta / Pracoviště MU

Přírodovědecká fakulta Fakulta informatiky Ústav výpočetní techniky Středoevropský technologický institut

Citace
WWW http://aip.scitation.org/doi/abs/10.1063/1.4978296
Doi http://dx.doi.org/10.1063/1.4978296
Obor Informatika
Klíčová slova Conformational dynamics; Free energy; Eigenvalues; Low dimensional topology; Biomolecular conformation;Approximation
Popis Metadynamics is an important collective-coordinate-based enhanced sampling simulation method. Its performance depends significantly on the capability of collective coordinates to describe the studied molecular processes. Collective coordinates based on comparison with reference landmark structures can be used to enhance sampling in highly complex systems; however, they may slow down simulations due to high number of structure-structure distance (e.g., mean-square deviation) calculations. Here we introduce an approximation of root-mean-square or mean-square deviation that significantly reduces numbers of computationally expensive operations. We evaluate its accuracy and theoretical performance gain with metadynamics simulations on two molecular systems. Published by AIP Publishing.
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