iSGTW - International Science Grid This Week
iSGTW - International Science Grid This Week

Home > iSGTW - 22 October 2008 > iSGTW Image of the week - Molecular dynamics simulation on DEISA infrastructure

Image of the week - Molecular dynamics on DEISA: lipids, licorice and lines

A single snapshot of a coarse-grained molecular dynamics simulation of a protein (Synaptobrevin transmembrane domain) in a lipid bilayer. The protein is shown as licorice, lipids as lines and water as points. The red arrows show the user external forces applied interactively in the simulation. Here, the membrane anchoring of protein is probed by pulling on one particular side (on tryptophane residues).

Image courtesy of

From the DEISA Newsletter, Vol. 5, 2008

Coupled applications

Many complex systems can be viewed as sets of components that obey their own physical laws and interact weakly with one another. Code-coupling, which deals with multi-physics, multi-models and multi-scale numerical simulations, is well-suited for inter-disciplinary research projects in which different legacy codes cooperate within the whole coupled application.

Generally, due to the complexity of these applications, coupled codes run with a moderate efficiency on parallel machines such as the DEISA infrastructure. A Joint Research Activity team within DEISA has enhanced the coupled applications to work on DEISA resources so that research teams can tackle new classes of numerical investigations.

As an example, large-scale computer simulations of biological systems provide valuable insight into molecular processes as diverse as enzymatic catalysis and membrane fusion.

Researchers at the theoretical biochemistry laboratory at the Institut de Biologie Physico-Chimique in Paris have used the visualization tool VMD to drive their GROMACS molecular dynamics simulations that examine the mechanical properties of (macro) molecules and their assemblies.


 iSGTW 22 December 2010

Feature – Army of Women allies with CaBIG for online longitudinal studies

Special Announcement - iSGTW on Holiday

Video of the Week - Learn about LiDAR


NeHC launches social media

PRACE announces third Tier-0 machine

iRODS 2011 User Group Meeting

Jobs in distributed computing


Enter your email address to subscribe to iSGTW.


 iSGTW Blog Watch

Keep up with the grid’s blogosphere

 Mark your calendar

December 2010

13-18, AGU Fall Meeting

14-16, UCC 2010

17, ICETI 2011 and ICSIT 2011

24, Abstract Submission deadline, EGI User Forum


January 2011

11, HPCS 2011 Submission Deadline

11, SPCloud 2011

22, ALENEX11

30 Jan – 3 Feb, ESCC/Internet2


February 2011

1 - 4, GlobusWorld '11

2, Lift 11

15 - 16, Cloudscape III

More calendar items . . .


FooterINFSOMEuropean CommissionDepartment of EnergyNational¬†Science¬†Foundation RSSHeadlines | Site Map