Guided Optimization Method for Fast and Accurate Atomic Charges
Computation

D 2016

Guided Optimization Method for Fast and Accurate Atomic Charges Computation

PAZÚRIKOVÁ, Jana, Aleš KŘENEK a Luděk MATYSKA

Základní údaje

Originální název

Guided Optimization Method for Fast and Accurate Atomic Charges Computation

Autoři

PAZÚRIKOVÁ, Jana (703 Slovensko, garant, domácí), Aleš KŘENEK (203 Česká republika, domácí) a Luděk MATYSKA (203 Česká republika, domácí)

Vydání

Ghent, Belgicko, Proceedings of the 2016 European Simulation and Modelling Conference, od s. 267-274, 8 s. 2016

Nakladatel

EUROSIS - ETI

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Belgie

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Kód RIV

RIV/00216224:14330/16:00091643

Organizační jednotka

Fakulta informatiky

ISBN

978-90-77381-95-3

Klíčová slova anglicky

optimization problem; computational chemistry; atomic charges; local vs. global optimization

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 11. 2016 10:54, Mgr. Aleš Křenek, Ph.D.

Anotace

V originále

Current advances in hardware and algorithm develop- ment allow the life science researchers to replace the experiment with a computer simulation. A key ob- ject of these computations is a molecule - a group of atoms interconnected via a cloud of electrons. For its computational processing, electrons around the atom are often represented by one number: partial atomic charge. It can be calculated by quantum mechan- ics (QM), which offers high accuracy at the cost of long computation time, or markedly faster by empirical methods such as Electronegativity Equalization Method (EEM). Empirical methods calibrate their parameters to the particular QM charge calculation approach by multi-dimensional optimization procedure. This work systematically summarizes and compares the accuracy and computational performance of available EEM pa- rameterization approaches with local, global or com- bined optimization (least squares, evolutionary and ge- netic algorithms). Moreover, we propose a new method- ology called guided minimization. We found that local optimization plays a crucial role in the parametrization, and only methodologies combining a global and a lo- cal optimization provide high-quality EEM parameters. Furthermore, we observed that global iterations of evo- lutionary of genetic algorithm often do not contribute to the result. Therefore, we reduced the global search method to guided minimization that achieves same or better accuracy than state-of-the-art methods and sur- passes them with simplicity and speed.

Návaznosti

LM2015085, projekt VaV

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

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

MUNI/A/0945/2015, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V.

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Přiložené soubory

OPT_04.pdf

Požádat o autorskou verzi souboru

paper.pdf

Vyhledat podobné dokumenty

ESM2016-1.pdf

Požádat o autorskou verzi souboru

Citovat

PAZÚRIKOVÁ, Jana, Aleš KŘENEK a Luděk MATYSKA. Guided Optimization Method for Fast and Accurate Atomic Charges Computation. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgicko: EUROSIS - ETI, 2016, s. 267-274. ISBN 978-90-77381-95-3.

@inproceedings{1360275,
   author = {Pazúriková, Jana and Křenek, Aleš and Matyska, Luděk},
   address = {Ghent, Belgicko},
   booktitle = {Proceedings of the 2016 European Simulation and Modelling Conference},
   editor = {José Évora-Gómez and José Juan Hernandéz-Cabrera},
   keywords = {optimization problem; computational chemistry; atomic charges; local vs. global optimization},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Ghent, Belgicko},
   isbn = {978-90-77381-95-3},
   pages = {267-274},
   publisher = {EUROSIS - ETI},
   title = {Guided Optimization Method for Fast and Accurate Atomic Charges Computation},
   year = {2016}
}

TY  - JOUR
ID  - 1360275
AU  - Pazúriková, Jana - Křenek, Aleš - Matyska, Luděk
PY  - 2016
TI  - Guided Optimization Method for Fast and Accurate Atomic Charges Computation
PB  - EUROSIS - ETI
CY  - Ghent, Belgicko
SN  - 9789077381953
KW  - optimization problem
KW  - computational chemistry
KW  - atomic charges
KW  - local vs. global optimization
N2  - Current advances in hardware and algorithm develop- ment allow the life science researchers to replace the experiment with a computer simulation. A key ob- ject of these computations is a molecule - a group of atoms interconnected via a cloud of electrons. For its computational processing, electrons around the atom are often represented by one number: partial atomic charge. It can be calculated by quantum mechan- ics (QM), which offers high accuracy at the cost of long computation time, or markedly faster by empirical methods such as Electronegativity Equalization Method (EEM). Empirical methods calibrate their parameters to the particular QM charge calculation approach by multi-dimensional optimization procedure. This work systematically summarizes and compares the accuracy and computational performance of available EEM pa- rameterization approaches with local, global or com- bined optimization (least squares, evolutionary and ge- netic algorithms). Moreover, we propose a new method- ology called guided minimization. We found that local optimization plays a crucial role in the parametrization, and only methodologies combining a global and a lo- cal optimization provide high-quality EEM parameters. Furthermore, we observed that global iterations of evo- lutionary of genetic algorithm often do not contribute to the result. Therefore, we reduced the global search method to guided minimization that achieves same or better accuracy than state-of-the-art methods and sur- passes them with simplicity and speed.
ER  -

PAZÚRIKOVÁ, Jana, Aleš KŘENEK a Luděk MATYSKA. Guided Optimization Method for Fast and Accurate Atomic Charges Computation. In José Évora-Gómez and José Juan Hernandéz-Cabrera. \textit{Proceedings of the 2016 European Simulation and Modelling Conference}. Ghent, Belgicko: EUROSIS - ETI, 2016, s.~267-274. ISBN~978-90-77381-95-3.

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