Implementation and Testing of Multiple Walkers Approach Based
Free Energy Calculations in the Grid Environment

D 2009

Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment

STŘELCOVÁ, Zora, Petr KULHÁNEK, Jan KMUNÍČEK, Jaroslav KOČA, Luděk MATYSKA et. al.

Basic information

Original name

Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment

Authors

STŘELCOVÁ, Zora, Petr KULHÁNEK, Jan KMUNÍČEK, Jaroslav KOČA and Luděk MATYSKA

Edition

Bratislava, Slovakia, GCCP Proceedings, p. 29-36, 7 pp. 2009

Publisher

Institute of Informatics SAS

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10403 Physical chemistry

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Organization unit

Faculty of Science

ISBN

978-80-970145-1-3

Keywords in English

free energy; adaptive biasing force method; multiple walkers approach; pseudorotaxanes; molecular shuttle; cucurbit[n]urils; VOCE; MetaCentrum

Abstract

V originále

The calculation of free energy is a challenging task because it requires very long molecular simulations to obtain converged and reliable results. To overcome this so called sampling problem, several methods have been developed. In this work, Adaptive Biasing Force (ABF) method and Multiple Walkers Approach (MWA) are used in the study of molecular shuttle in pseudorotaxane complexes and water molecule transit through cucurbit[n]uril cavity. ABF method improves sampling by biasing system along a predefined reaction coordinate, which describes studied process. The sampling is further improved by MWA, which exchanges reconstructed free energy potential among several independent simulations (walkers) biased by ABF. Exchanges with all walkers need not be necessarily synchronized therefore it is possible to speed up the whole calculation in almost linear fashion. Due to this feature the combination of both methods is suitable for utilization within the production grid environment. Our tests were performed in the two distinct grid environments (VOCE and MetaCentrum ) and subsequently validated that MWA/ABF approach is promising tool benefiting from run in any Grid.

Links

LC06030, research and development project

Name: Biomolekulární centrum

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre

MSM0021622413, plan (intention)

Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment

MSM6383917201, plan (intention)

Name: Optická síť národního výzkumu a její nové aplikace

Citovat

STŘELCOVÁ, Zora, Petr KULHÁNEK, Jan KMUNÍČEK, Jaroslav KOČA and Luděk MATYSKA. Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment. In GCCP Proceedings. Bratislava, Slovakia: Institute of Informatics SAS, 2009, p. 29-36, 7 pp. ISBN 978-80-970145-1-3.

@inproceedings{862752,
   author = {Střelcová, Zora and Kulhánek, Petr and Kmuníček, Jan and Koča, Jaroslav and Matyska, Luděk},
   address = {Bratislava, Slovakia},
   booktitle = {GCCP Proceedings},
   keywords = {free energy; adaptive biasing force method; multiple walkers approach; pseudorotaxanes; molecular shuttle; cucurbit[n]urils; VOCE; MetaCentrum},
   language = {eng},
   location = {Bratislava, Slovakia},
   isbn = {978-80-970145-1-3},
   pages = {29-36},
   publisher = {Institute of Informatics SAS},
   title = {Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment},
   year = {2009}
}

TY  - JOUR
ID  - 862752
AU  - Střelcová, Zora - Kulhánek, Petr - Kmuníček, Jan - Koča, Jaroslav - Matyska, Luděk
PY  - 2009
TI  - Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment
PB  - Institute of Informatics SAS
CY  - Bratislava, Slovakia
SN  - 9788097014513
KW  - free energy
KW  - adaptive biasing force method
KW  - multiple walkers approach
KW  - pseudorotaxanes
KW  - molecular shuttle
KW  - cucurbit[n]urils
KW  - VOCE
KW  - MetaCentrum
N2  - The calculation of free energy is a challenging task because it requires very long molecular simulations to obtain converged and reliable results. To overcome this so called sampling problem, several methods have been developed. In this work, Adaptive Biasing Force (ABF) method and Multiple Walkers Approach (MWA) are used in the study of molecular shuttle in pseudorotaxane complexes and water molecule transit through cucurbit[n]uril cavity. ABF method improves sampling by biasing system along a predefined reaction coordinate, which describes studied process. The sampling is further improved by MWA, which exchanges reconstructed free energy potential among several independent simulations (walkers) biased by ABF. Exchanges with all walkers need not be necessarily synchronized therefore it is possible to speed up the whole calculation in almost linear fashion. Due to this feature the combination of both methods is suitable for utilization within the production grid environment. Our tests were performed in the two distinct grid environments (VOCE and MetaCentrum ) and subsequently validated that MWA/ABF approach is promising tool benefiting from run in any Grid.
ER  -

STŘELCOVÁ, Zora, Petr KULHÁNEK, Jan KMUNÍČEK, Jaroslav KOČA and Luděk MATYSKA. Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment. In \textit{GCCP Proceedings}. Bratislava, Slovakia: Institute of Informatics SAS, 2009, p.~29-36, 7 pp. ISBN~978-80-970145-1-3.

Detailed Information on Publication Record