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

J 2017

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

PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK a Mária ŠIMKOVÁ

Základní údaje

Originální název

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

Autoři

PAZÚRIKOVÁ, Jana (703 Slovensko, garant, domácí), Aleš KŘENEK (203 Česká republika, domácí), Vojtěch SPIWOK (203 Česká republika) a Mária ŠIMKOVÁ (703 Slovensko, domácí)

Vydání

Journal of Chemical Physics, Melville, American Institute of Physics, 2017, 0021-9606

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.843

Kód RIV

RIV/00216224:14610/17:00094853

Organizační jednotka

Ústav výpočetní techniky

DOI

http://dx.doi.org/10.1063/1.4978296

UT WoS

000397313600032

Klíčová slova anglicky

Conformational dynamics; Free energy; Eigenvalues; Low dimensional topology; Biomolecular conformation;Approximation

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 6. 4. 2018 18:06, Ing. Jana Hozzová, Ph.D.

Anotace

V originále

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.

Návaznosti

GA15-17269S, projekt VaV

Název: Simulace komplexních systémů se zesíleným vzorkováním

Investor: Grantová agentura ČR, Simulace komplexních systémů se zesíleným vzorkováním

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

Citovat

PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK a 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, roč. 146, č. 11, s. "115101:1"-"115101:8", 8 s. ISSN 0021-9606. Dostupné z: https://dx.doi.org/10.1063/1.4978296.

@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 a 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, roč.~146, č.~11, s.~''115101:1''-''115101:8'', 8 s. ISSN~0021-9606. Dostupné z: https://dx.doi.org/10.1063/1.4978296.

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