Detailed Information on Publication Record
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
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
Tags
International impact
Změněno: 10/4/2010 11:08, prof. RNDr. Jaroslav Koča, DrSc.
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 |
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MSM0021622413, plan (intention) |
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MSM6383917201, plan (intention) |
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