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Computer Cluster

Computer ClusterIn addition to computers located in individual laboratories, the Department has a dedicated Computer Cluster consisting of 16 Pentium computers and 2 laserprinters that are available for use by both undergraduate and graduate students, as part of their instructional and research activities.

Use of these computers is integrated into the entire undergraduate curriculum, beginning with the "Principles of Chemistry" course taken by freshman, through the senior "Seminar" course.

Each computer is equipped with high-speed internet connectivity and appropriate software needed for classroom and/or research needs, including applications such as
  • Microsoft Office
  • Corel WordPerfect
  • Sigma Plot
  • Bio-Rad Laboratories ChemWindow Suite
  • Molecular Visualization Programs
  • Internet Explorer

West Center for Computational Chemistry and Drug Design

The West Center for Computational Chemistry and Drug Design was established by an initial gift to the University from the West Foundation in 1999 for the support of Computational Chemistry, especially as applied to Drug Discovery, or as it is also referred, Drug Design.

The original gift, plus a second gift in 2002, in combination with support from the University, has allowed us to renovate a classroom and purchase a variety of computer systems dedicated to computational chemistry, including stand alone PC's, i-Macs, Mac G4's and G5's, servers, Silicon Graphics Workstations and Beowulf Supercomputer Clusters (see below). Most of the original computers have since been replaced with newer, more powerful computers (picture is of the West Center as it existed in 2002).

A variety of sophisticated software packages are also available in the West Center, including Oracle, Gaussian 98 and AMBER, which allow database management of both chemical and genetic databases, as well as greatly improved computer modeling capabilities.

Drs. Moore (West Center Director), Li, Moyna, Pophristic and Zauhar, are all heavily involved in the continued improvements to, and operation of the West Center.

Beowulf "Supercomputer" Clusters - What do they do?

West Center ClustersThe Department currently has four Beowulf Supercomputer Clusters in operation, including the original 20-processor cluster (now upgraded wtih new and faster processors), along with a 32-processor and two 128-processor clusters which are located in a separate machine room. These Beowulf Clusters are configured with the individual processors operating in parallel, so that simultaneious operations can take place. Parallel-processing computer clusters are designed for problems that can be broken up into small tasks, each of which can be accomplished on the single processor of an ordinary PC. By then combining the completed tasks of all the individual processors in the cluster, very large, complex computations can be completed in a relatively short time. Additional detail is provided below, but if you would like more information about these kind of computers and how they are used in research, please contact either Dr. Preston Moore, the West Center Director, or Dr. Guillermo Moyna.

The original 20-processor cluster (upgraded with newer, and faster processors) and one of the newer 128-processor clusters are shown above (with Dr. Ed Birnbaum, the Department Chair sandwiched in between). Both Beowulf clusters occupy about the same amount of space, but with greatly different computational power.

These powerful computers are used by computational chemists to model and display all different kinds of chemical systems; anything from the structure of a very small molecule such as aspirin, to a very large molecule such as the protein HIV protease. The software packages available in the West Center allow faculty and students to carry out complex calculations which simulate the charge attractions and repulsions that exist between the atoms that make up molecules, as well as the stretching and bending of the chemical bonds within a molecule. Complex molecular systems can be modeled in the gas phase, or in solution, where interactions between solvent molecules must also be incorporated, or in the solid state.

West CenterIn addition to modeling a specific molecular structure, these computational methods can also be used to evaluate how two molecules, such as a potential drug and it's receptor protein, are likely to interact. This is a powerful tool for the design of new drugs. In the picture to the right, Dr. Liu is reviewing the results of her calculation, which was carried out on one of the West Center's 128-processor Beowulf clusters.

 

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