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Managing Molecular Dynamics Simulations

The Application Hosting Environment, commissioned by OMII-UK, is a lightweight hosting environment for running unmodified scientific applications. AHE builds a layer of middleware on top of existing technologies such as Globus, interacting with computational resources via the OMII-UK GridSAM job submission web service. AHE is a GridSAM client, generating and submitting the JSDL job descriptions consumed by GridSAM.

AHE has users within several UK academic institutions, making use of the AHE to run production scientific simulations on the National Grid Service, including HPCx; indeed the NGS was the first grid on which the AHE was deployed. In addition, the AHE is also being used to run simulations on the US TeraGrid and a centralised deployment is currently under consideration at some TeraGrid sites [11].

The GridSAM interface means that AHE can be used to provide a uniform interface to any computational resource for which GridSAM has a Distributed Resource Manager (DRM) connector. The nature of the AHE, and its reliance on GridSAM, means that it creates a user perceived, federated grid of resources, allowing access to any grid to which the AHE is configured to submit to and the user is authorised to use.

The key benefit of using GridSAM is that AHE, and by extension its users, are shielded from the variance between underlying grid middlewares, and can get on with scientific work rather than learning the details of the grid middleware in use on any particular grid.

AHE currently hosts a wide range of scientific applications including NAMD, LB3D, LAMMPS, DL_POLY, on remote grid resources. AHE builds a layer of middleware on top of existing technologies such as Globus, abstracting the details of the particular underlying grid middleware in use. It does this by representing applications as stateful web services using WSRF::Lite, a Perl implementation of the WSRF specification. AHE interacts with computational resources via the OMII GridSAM job submission web service, generating and submitting the JSDL job descriptions consumed by GridSAM.

AHE has been instrumental in facilitating investigations conducted within the Centre for Computational Science at UCL into the molecular dynamics of HIV-1 protease. The number of clinically interesting drug resistant mutational patterns is far larger than the available crystal structures of HIV-1 protease. Mutational protocols convert one protease sequence with available crystal structure into another that diverges by a small number of mutations. It is important that such mutational algorithms are followed by suitable multi-step equilibration protocols, using chained molecular dynamics simulations, to ensure that the desired mutant structure is an accurate representation. Previously these have been difficult to perform on computational grids due to the need to keep track of large numbers of simulations. We have successfully used AHE to manage all of the simulations required to construct a chained simulation, scripting AHE command line clients to create complex application workflows, linking the output of one simulation into the input of the next. This approach has greatly simplified the scientist life, reducing the time taken tracking and marshalling input and output files between remote grid resources.