Molecular Mechanics with an Array Processor.
Abstract
In recent years molecular mechanics, the computer simulation of molecular systems using molecular dynamics, Monte Carlo, and energy minimization, has emerged as a powerful tool for investigating and understanding chemical properties and processes. In this paper we discuss a particular solution to the computational needs of molecular mechanics, the use of specialized hardware, a high speed array processor, in our case a Floating Point Systems, Inc. AP-120B. In other papers, we have also discussed an alternative solution, the division of the problem among an array of different processors operating in parallel. Yet a third solution is to use a vector processing machine such as a Cray-1. We will focus here primarily on molecular dynamics within the array processor program package for molecular mechanics we have developed, called Newton. In section II we examine the architecture of the AP-120B. In section III we lay out the specifics of the structure of the program package we have developed for molecular dynamics. Finally, in section IV we present the results, analyze potential array processor improvements, and point out the advantages and importance of the environment in terms of language and operating system.
Document Details
- Document Type
- Technical Report
- Publication Date
- Jun 01, 1982
- Accession Number
- ADA117070
Entities
People
- Kent R. Wilson
- Peter H. Berens
Organizations
- University of California, San Diego