Five in focus, Spring 2007

Enabling computational and experimental chemists to easily do computational chemistry by providing a cyberinfrastructure scientists can access from their own desktop computers is the driving force behind the Computational Chemistry Grid (CCG). CCG is a virtual organization that provides access to high-performance computing resources for computational chemistry with intuitive interfaces and measurable quality of service. User support and user services are also provided.

1. Client inferface. Running Java on their desktop computer, CCG users utilize GridChem, an easy to maneuver client interface, to access the network through a secure Internet portal. The GridChem interface integrates the hardware, software, and middleware resources necessary to solve computational chemistry problems using grid technologies.

2. Manage jobs. GridChem allows users to submit and monitor jobs run on any computer on which they have an allocation, without having to log in to each system or to remember the unique features of each system. Files are staged automatically.

3. Resource allocations. Last year, 100 researchers used more than 335,000 service units of computing time. Jobs are automatically dispatched to available CGG resources.

4. Download results and post-process review. Results are downloaded to the user's desktop machine. After the computation is completed, users need to extract information from the output files. Usually, the output information is determined by research parameters such as software applied, type of calculation, theory level, and so forth.

5. Educational benefits. The simplified interface of the GridChem tools makes it easy to build models or create molecular simulations. Tools can be combined via Web pages to create virtual "lab assignments" for courses.

1. Computational chemistry a click away

GridChem uses well established grid technologies to provide chemists access to cyberinfrastructure (software, hardware, and services). A self-contained desktop client for input editing, job submission to remote HPC sites, and job management and post-processing for computational chemistry applications, GridChem is portable, adaptable to other applications, easy to install, and does not require installation of any grid software on the desktop system. Clients include expert, novice, and non-traditional users in both computational and experimental chemistry.

By using GridChem and the computing resources of the CCG, Robert Bach and Olga Dmitrenko, researchers at the University of Delaware, were able to complete a series of model theoretical calculations that suggests a new mechanism for the oxidation step in enzymatic cytochrome P450 hydroxylation of saturated hydrocarbons. "Such calculations involving structures with 500-600 basis functions are simply not feasible utilizing local work stations available at my university," says Bach. "The potential for several electronic states (doublet vs. quartet) increases the amount of computing power necessary to study such complex problems." Their work is supported by NSF.

P450 is an enzyme in the liver that breaks down carbohydrates, fats, and other things that contain hydrocarbons, such as steroid drugs, into metabolites. How P450 breaks down a drug affects how it works. Learning more about how P450 acts can lead to better, more effective medicines.

The CCG/GridChem project is a NSF three-year National Middleware Initiative program now in its third year. NCSA was a key player in the initial development of the GridChem client software and middleware. It is the middleware that makes this project feasible. "The middleware hides all the complexity of the grid, the distributed cyberinfrastructure, and provides an intuitively-simple interface to the end-user chemist," explains Sudhaker Pamidighantam, an NCSA research scientist involved in the development of GridChem. He now provides support to GridChem users, and helped Bach and Dmitrenko solve some problems with code.

Other project partners are: the Ohio Supercomputing Center (Ohio State University), the Center for Computational Sciences (University of Kentucky), the Center for Computation and Technology (Louisiana State University), and the Texas Advanced Computing Center (University of Texas).

NCSA NEWS

Five in focus, Spring 2007