Publication details

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

Authors

PAZÚRIKOVÁ Jana KŘENEK Aleš SPIWOK Vojtěch ŠIMKOVÁ Mária

Type Article in Periodical
Magazine / Source Journal of Chemical Physics
MU Faculty or unit

Institute of Computer Science

Citation
Web http://aip.scitation.org/doi/abs/10.1063/1.4978296
Doi http://dx.doi.org/10.1063/1.4978296
Field Informatics
Keywords Conformational dynamics; Free energy; Eigenvalues; Low dimensional topology; Biomolecular conformation;Approximation
Description 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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