Speaker
Description
Summary
Advances in the Grid enabled molecular simulator (GEMS)
The EGEE project supports the deployment of the CompChem VO
services and infrastructure on
behalf of the Computational Chemistry virtual community. The key
commitment of the CompChem
VO is the design and the implementation of the Grid Enabled
Molecular Simulator (GEMS)[1] and
its deployment on the EGEE production Grid environment (see the
related Memorandum of
Understanding between EGEE and CompChem at the URL
http://compchem.unipg.it). The main
goal of GEMS is the ab initio calculation of the properties of
molecular systems by allowing the
researcher to perform the various computational steps from a
single portal. The GEMS portal is
structured as a work-flow of distributed suites of programs
ranging from the ab initio calculation of electronic structures
and energies, the evaluation of the parameters of a given
functional representation of the interaction best fitted to the
ab initio points, the integration of motion equations using
either quantum or quasi- and semi-classical means, to the
reconstruction of experimental observables from ab initio
information.
Depending on the intrinsic complexity of the molecular system
considered and the computational
approach used, the workload of the required tasks may vary
significantly in terms of complexity,
number and sequence. For this reason GEMS programs represent a
suitable test bed to exploit the characteristics of the EGEE Grid
infrastructure.
Several Computational procedures have been structured to run in
parallel (using MPICH message
passing APIs) in the Grid. The benchmarks performed show
excellent performances on the Grid
environment [2]. In particular, extended computational campaigns
were carried out by the
Laboratory of Physical Chemistry of the University of the Basque
Country in Vitoria (ES) to
calculate some properties of the OH+CO reaction at low energy
using Quasiclassical
approaches. The results of such a campaign contributed to the
understanding of this important
system for the combustion of hydrocarbons with air[3]. In the
next months the campaign will be
extended to Quantum Time Dependent approaches[4].
To enhance the capability of rationalizing the outcomes of a
given reactive process, a set of virtual monitors have been
implemented. They allow the researcher to study visually the
evolution of a given simulation and to represent, using Web3D
technologies, some interesting or crucial phases of the
investigated process[2]. In the Virtual Laboratory the
intermediate data of the simulation are interpreted and
transformed into an X3D virtual world that represents the related
Molecular Virtual Reality (MVR) scene. The researcher can
interact with the MVR world and control some visualization
aspects of the scene. She/He can also navigate inside the virtual
world made by atoms and bonds. The use of immersive devices (like
data gloves, motion trackers and head mounted displays) has also
been implemented. In addition some virtual monitors have been
implemented as Web or Grid services. In this way, the
applications can invoke the visualization tools in a standardized
way. This facilitates the work of the users when writing
applications or customizing them, since it provides a standard
method to access virtual reality environments and visualization
tools [5].
In the near future CompChem will also increase the number and
types of
partner laboratories and establish strict links with the just
launched COST Action D37
"GridChem" as well. Some Grid technology transfer activities to
the Theoretical and Computational Chemistry group of the
University of Crete will also be developed within the ENACTS project.
References
[1] O. Gervasi, C. Dittamo and A. Laganà, A Grid Molecular
Simulator for E-Science, Lecture Notes in Computer Science, 3470,
pp. 16-22 (2005); A. Laganà, A. Riganelli and O.
Gervasi, On the Structuring of the Computational Chemistry
Virtual Organization
CompChem, Lecture Notes in Computer Science, 3980, pp.665-674 (2006)
[2] O. Gervasi and A. Laganà, A Priori Molecular Virtual reality
on EGEE Grid, Journal of
Grid Computing, Springer, (2006), in press.
[3] E.Garcia, A.Saracibar, C.Sanchez, A.Laganà, A multiproperty
analysis of the OH +
H2(D2,HD)} potential energy surface, Chemical Physics 308,
201-210 (2005); A.Rodriguez,
E.Garcia, M.L.Hernandez, A.Lagana, Isotopic effects in the
product vibrational distribution
of OH(OD)+HCl} reaction, Chemical Physics Letters 371, 223-228
(2003).
[4] D. Skouteris, L. Pacifici, A. Laganà, Time dependent
wavepacket calculations for the N + N2 system on a LEPS surface:
inelastic and reactive probabilities, Mol. Phys. 102 (21-22),
2237 - 2248 (2004)
[5] O. Gervasi, S. Tasso and A. Laganà, Immersive Molecular
Virtual Reality based on X3D
and Web Services, Lecture Notes in Computer Science, 3980,
pp.212-221 (2006)