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Integrated Applications in Scientific Computing

© Adam Hughes

Over the last few months, the articles in this space have covered many important and disparate topics relevant to the scientist who relies, at least in part, on computers to conduct his research. It seems appropriate at this juncture to see how the different components we've explored can come together to form very powerful research tools. For this purpose, we'll harken back to our old friend, computational chemistry, and look at the offerings of Molecular Simulations, Inc.

Molecular Simulations, Inc. (MSI), located in San Diego, is one of the industry leaders in providing simulation tools to chemistry researchers around the world. While lots of other companies and universities provide chemistry software, MSI is definitely the most ambitious, and their products serve as sleek examples of an integrated package incorporating the best that modern computer science has to offer.

There are two widely used MSI products, one called Insight, the other Cerius. There are some substantive differences between the two packages; but for our purposes, it's safe to assume that they are interchangeable. The main "hook" for these programs is that they allow the scientist to set up and run his problem using a sophisticated graphical user interface (GUI). The researcher can use built-in utilities to build just about any molecule he wants and render the results in a number of pleasing and insightful ways. These GUI's are meant to be user-friendly, and for the most part, they are. With a minimum amount of instruction, a new user can sit down and set up his desired system in a reasonable period of time.

Having established a model to work with the researcher need not leave the program to complete the study he has in mind. From the same GUI he used to build his system, the scientist can run programs that incorporate any number of simulation techniques. Some of these programs are even parallelized and can thus take advantage of the power of supercomputers. If there is a question about some utility, a click of the mouse can bring the answers. If the "help" function directly accessible from the program GUI doesn't sufficiently resolve the problem, it's likely an answer can be found in the documentation available at MSI's well-stocked home page.

Another feature of the MSI software packages that fits in neatly with one of the main thrusts of these articles is that both Unix and PC platforms are supported. The balance between the two is constantly evolving with the changing computing landscape.

As one of the many companies offering chemistry simulation software, MSI presents a package of software based on integrated

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