GridMACS Portal: A Grid Web Portal for Molecular Dynamics Simulation Using GROMACS

We developed GridMACS, a grid-enabled web portal with the aim of providing GUI for GROMACS and running a molecular dynamics simulation in a grid environment. The portal is developed according to the basic grid system architecture by integrating the main grid layers such as the Gridsphere Portal Framework, Vine Toolkit (grid service) and Globus Toolkit (grid middleware). The integration with the computing resources was achieved by the deployment of the main grid layers on a cluster grid environment. Creation of this portal will provide a GUI based user-friendly environment that will assist biologist in providing them the availability and usability. GridMACS will serve as an initial proof of concept and in the future will subsequently become a platform for other bioinformatics tools to be implemented on a grid platform as a port let application. The portal is easily accessible via the internet on any browsers at www.gridmacs.fbb.utm.my:8080/gridsphere/gridsphere.