Feb 11 – 14, 2008
<a href="http://www.polydome.org">Le Polydôme</a>, Clermont-Ferrand, FRANCE
Europe/Zurich timezone

The study of Cytochrome C oxidase on EGEE Grid

Feb 11, 2008, 5:00 PM
20m
Auvergne (<a href="http://www.polydome.org">Le Polydôme</a>, Clermont-Ferrand, FRANCE)

Auvergne

<a href="http://www.polydome.org">Le Polydôme</a>, Clermont-Ferrand, FRANCE

Oral Scientific Results Obtained Using Grid Technology Computational Chemistry & Material Science

Speaker

Dr Osvaldo Gervasi (Dept. of Mathematics and Computer Science, University of Perugia)

Description

The current project involves Molecular Dynamics calculations on cytochrome c oxidase. CcO is the terminal enzyme of respiratory chains found in the inner mitochondrial membranes or in many bacteria and the last acceptor of electrons from oxidizing processes involving nutrient molecules. The biophysical interest of this project stems on long standing problems which concern the assignment of difference spectra of isotopically substituted ferryl oxygen.

1. Short overview

Our Grid experience carrying out Molecular Dynamics calculations on the enzyme
cytochrome c oxidase (CcO) on EGEE through Compchem VO will be presented and
discussed. The biomolecule (CcO) consists of approximately 10000 atoms and the
calculations would require years of our local CPU time. Performances and
drawbacks of the current status of the Grid will be discussed.

4. Conclusions / Future plans

The paper reports our experience in studying the spectroscopy and reaction
dynamics of enzymes with classical dynamics on the production EGEE Grid
environment using the HellasGrid and CompChem and SEEGrid VOs.

URL for further information:

http://tccc.iesl.forth.gr
http://compchem.unipg.it

Provide a set of generic keywords that define your contribution (e.g. Data Management, Workflows, High Energy Physics)

Computational Chemistry, Dynamics and Spectroscopy of Proteins, Classical Molecular
Dynamics

3. Impact

The Molecular Dynamics calculations on cytochrome c oxidase is a heavily
demanding application in terms of the CPU time required. Furthermore, it is
demonstrated that the study of the vibrational spectra and dynamics for
pumping water molecules from the active site, it presents a perfect example
for a Grid application. We performed the domain decomposition of the initial
conditions and a large number of sequential jobs have been launched on the Grid.

To this end, the computer codes running on our local clusters were gridified
and some scripts were written to make the Grid calculations feasible,
automating the management of the large number of jobs.
Some errors occurred in the scheduling of the jobs have been managed
resubmitting the failed ones automatically.
The large number of CPUs available on HellasGrid and on Compchem and SEEGrid VOs made it possible to perform the preliminary production runs, while the project
is still in progress.

Primary authors

Dr Manos Giatromanolakis (Institute of Structure and Lasers, Foundation for Research and Technology-Hellas) Dr Osvaldo Gervasi (Dept. of Mathematics and Computer Science, University of Perugia) Prof. Stavros C. Farantos (Department of Chemistry, University of Crete, Iraklion 711 10 and Institute of Electronic Structure and Lasers, Foundation for Research and Technology-Hellas) Dr Vangelis Daskalakis (Institute of Structure and Lasers, Foundation for Research and Technology-Hellas)

Presentation materials