Crunch software

No excuses. Anyone who has passed a course in physical chemistry should be able to crunch this book for numbers and for equations. Engineers can treat it as a handbook with long explanations whose formulae can be plugged into original programs or packaged software (preferably both so as to understand what is being computed). 

We have described some of the software that already exists and which already is applicable to investigations of protein structure. But if these calculations can already be accomplished, why do we need supercomputers In some cases, such as molecular dynamics, the question is one of brute number-crunching power — a faster computer will permit simulations of the motions of larger molecules over longer time intervals. But in other cases the question is not one of feasibility vs. infeasibility of the calculation, but in the speed with which the calculation can be completed relative to the time scale of interactive computing. Supercomputers may, in some cases, be able to convert certain tasks that must currently be run in batch mode to tasks that can be run interactively. This opens new doors. 

The emergence of molecular modeling and computational into a discipline has been closely associated with advances in computer hardware, computer graphics, and software. The availability of more sophisticated number-crunching power has allowed scientists to calculate the properties oflarger and larger molecules. With the advent of supercomputers, dynamics calculations on biomolecules surrounded by an environment of water are becoming common. 

Crunch http //www.bfsc.leidenuniv.nl/software/crunch/... 

Engineers then refocused their task on two areas, how to reorganize the design process to take full advantage of the number crunching ability of the computer and how to design mathematical models that would be black-boxed into the computer s software. 

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