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 and Mária ŠIMKOVÁ

Basic information

Original name

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

Authors

PAZÚRIKOVÁ, Jana (703 Slovakia, guarantor, belonging to the institution); Aleš KŘENEK (203 Czech Republic, belonging to the institution); Vojtěch SPIWOK (203 Czech Republic) and Mária ŠIMKOVÁ (703 Slovakia, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 2.843

RIV identification code

RIV/00216224:14610/17:00094853

Organization unit

Institute of Computer Science

DOI

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

UT WoS

000397313600032

EID Scopus

2-s2.0-85015630113

Keywords in English

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

Abstract

In the original language

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.

Links

GA15-17269S, research and development project

Name: Simulace komplexních systémů se zesíleným vzorkováním

Investor: Czech Science Foundation

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

Cite

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.

@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.

Přehled o publikaci