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@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.
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