Description
The EGEE series of projects brought computational chemistry on a grid to a new level: from a small group of users to a second resource consumer just after High Energy Physics. Chemical applications on EGEE Grid cover a wide area ranging from quantum dynamics computations for small molecular systems through ab initio simulations up to molecular dynamics studies of huge molecular systems of biological and industrial importance.
The User Forum is an annual EGEE conference whose unique character descends from the fact that grid users can meet together with developers. This year dedicated oral talks and accompanying posters detail not only current development on the EGEE grid of the computational chemistry domain traditional subjects. Large part of the conference session is instead devoted to the rapid evolution of computational chemistry tools to the quickly approaching EGI era. Typical examples of this are web services enabling easy use of chemical software on the Grid or implementation of new techniques enabling computation of various energy derivatives โ crucial for determination of many molecular properties.
-
Dr Alessandro Costantini (COMPCHEM-University of Perugia)13/04/2010, 11:00Experiences from application porting and deploymentOralThe work carried out to implement complex computational chemistry suites of codes on distributed systems and, at the same time, to develop appropriate graphical tools for the visual rendering of the outcomes of the calculations on the production EGEE Grid infrastructure available to the COMPCHEM VO, is here presented and discussed with some examples.Go to contribution page
-
Dr Mariusz Sterzel (ACC Cyfronet AGH)13/04/2010, 11:20Experiences from application porting and deploymentOralChemical software, especially with ab initio methods, have been developed over several years of research in the field of numerical methods in chemistry. As the research was performed by many groups of scientists this resulted in a variety of software suites. From this set the commercial packages are of particular interest among the community due to the availability of many computational...Go to contribution page
-
Dr Sergio Rampino (Universitร degli Studi di Perugia)13/04/2010, 11:40Scientific results obtained using distributed computing technologiesOralWe have assembled on the COMPCHEM segment of the EGEE Grid Infrastructure the core of the Grid Empowered Molecular Simulator (GEMS) queueing in a common workflow a suite of - adequately "gridified" - codes for the a priori modeling of elementary chemical processes. The communication between applications from different scientific domains is fostered by the use of common data formats. A test...Go to contribution page
-
Dr Stefano Cozzini (CNR-INFM Democritos and ICTP)13/04/2010, 12:00
-
Mr Jiri Wiesner (Masaryk University)13/04/2010, 14:00Scientific results obtained using distributed computing technologiesOralOne of the most abundant quantities characterising proteins is its isoelectric point, which is directly dependent on the number of charged ionizable residues, on the pKa of all ionizable residues more exactly. In this work, the pKa of buried protein aminoacids are estimated using method based on molecular dynamics called thermodynamic integration. The main scope is to compute pKa in...Go to contribution page
-
Stavros Farantos (Foundation for Research and Technology-Hellas/ Institute of Electronic Structure and Laser)13/04/2010, 14:20Scientific results obtained using distributed computing technologiesOralAtomistic simulations of large biomolecules such as proteins require extensive computational resources. Dynamical and thermodynamical properties can be obtained either by averaging over very long time trajectories or sampling the phase space by running hundreds of short time trajectories. The latter methods are the most appropriate for high throughput computers such as the Grid distributed...Go to contribution page
-
Dr Dimitrios Skouteris (University of Perugia)13/04/2010, 14:40Scientific results obtained using distributed computing technologiesOralWe have embarked upon a project of performing dynamical calculations treating electrons and nuclei on exactly the same footing, considering all particles as degrees of freedom of a dynamical system. In that way, the Born-Oppenheimer approximation is circumvented. The very concept of a potential energy surface is abolished and the problems associated with kinetic energy couplings or Berry...Go to contribution page
-
Dr Fermin Huarte (University of Barcelona)13/04/2010, 15:00Scientific results obtained using distributed computing technologiesOralOur communication provides a detailed description of the present performance of grid-Fluss and grid/MCTDH, tools for the direct quantum-mechanical calculation of kinetic coefficients, implemented on the section of the production computing Grid of EGEE accessible to the COMPCHEM virtual organization. The performance and reliability of the method is illustrated by presenting the results of two...Go to contribution page