| PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK and Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. Journal of Chemical Physics. Melville: American Institute of Physics, 2017, vol. 146, No 11, p. "115101:1"-"115101:8", 8 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4978296. |
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@article{1386007,
author = {Pazúriková, Jana and Křenek, Aleš and Spiwok, Vojtěch and Šimková, Mária},
article_location = {Melville},
article_number = {11},
doi = {http://dx.doi.org/10.1063/1.4978296},
keywords = {Conformational dynamics; Free energy; Eigenvalues; Low dimensional topology; Biomolecular conformation;Approximation},
language = {eng},
issn = {0021-9606},
journal = {Journal of Chemical Physics},
title = {Reducing the number of mean-square deviation calculations with floating close structure in metadynamics},
url = {http://aip.scitation.org/doi/abs/10.1063/1.4978296},
volume = {146},
year = {2017}
}
TY - JOUR
ID - 1386007
AU - Pazúriková, Jana - Křenek, Aleš - Spiwok, Vojtěch - Šimková, Mária
PY - 2017
TI - Reducing the number of mean-square deviation calculations with floating close structure in metadynamics
JF - Journal of Chemical Physics
VL - 146
IS - 11
SP - "115101:1"-"115101:8"
EP - "115101:1"-"115101:8"
PB - American Institute of Physics
SN - 00219606
KW - Conformational dynamics
KW - Free energy
KW - Eigenvalues
KW - Low dimensional topology
KW - Biomolecular conformation;Approximation
UR - http://aip.scitation.org/doi/abs/10.1063/1.4978296
L2 - http://aip.scitation.org/doi/abs/10.1063/1.4978296
N2 - 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.
ER -
PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK and Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. \textit{Journal of Chemical Physics}. Melville: American Institute of Physics, 2017, vol.~146, No~11, p.~''115101:1''-''115101:8'', 8 pp. ISSN~0021-9606. Available from: https://dx.doi.org/10.1063/1.4978296.
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