AbstractComputer simulation of the mechanics of molecular systems is a popular and powerful method for understanding chemical processes. The complexity of modeled chemical systems has advanced from hard spheres and rare gases to liquid solutions and biomolecules. Such simulations are computationally intensive and thus are limited by the speed of available computers. This article describes the use of specialized hardware, a high‐speed floating‐point array processor (AP), to dramatically speed up molecular mechanics, in other words molecular dynamics, Monte Carlo, and energy‐minimization calculations. Although the array processor is a cost effective solution for computationally intensive problems in terms of hardware (full‐time AP usage is equivalent to 2–8 h/day of Cray‐1 time), its full speed comes at the expense of programming in a relatively difficult parallel assembly language. Since the architecture of the machine is dramatically different from conventional computers and utilizing its fast speed necessitates using this architecture on the assembly language level, the proper design and implementation of algorithms is critical. The molecular mechanics software design discussed here, consisting of 12,000 lines of C and 7000 lines of AP assembly language code, is quite general and has been used to study systems ranging from rare gases to biomolecules. This implementation yields effective speeds approximately 35 times faster than a dedicated DEC VAX 11/780 computer with floating‐point accelerator and optimized VMS FORTRAN, thus allowing simulations to be run in one and a half weeks on the AP which would require a year of dedicated VAX time. The flexibility of the UNIX operating system, whose source code is accessible and can be modified to optimize performance, combined with the modern features of the C language, have made this implementation much easier by providing a convenient and powerful environment in which to imbed the hand‐coded AP assembly language modules. Applications to date range from the molecular‐dynamic calculation of infrared, Raman, and electronic spectra in gas and liquid solutions to the calculation of thermodynamic quantities for water and the simulation of the molecular dynamics of solution reactions and polypeptides.
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