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From: briscoe-duke@CS.YALE.EDU (Duke Briscoe)
Newsgroups: bionet.molbio.proteins
Subject: Re: Special Computer for MD (In English)
Keywords: MD
Message-ID: <25511@cs.yale.edu>
Date: 5 Jul 90 16:02:04 GMT
References: <946@kudpc.kyoto-u.ac.jp>
Sender: news@cs.yale.edu
Reply-To: briscoe-duke@CS.YALE.EDU (Duke Briscoe)
Organization: Yale University Computer Science Dept, New Haven CT  06520-2158
Lines: 37

In article <946@kudpc.kyoto-u.ac.jp> e50214@kuduts.kudpc.kyoto-u.ac.jp (toshio nishigaki [e50214]) writes:
>
>	I am thinking of building a computer system for the exclusive use of MD
>(moleculer dynamics) simulation (presentry in my mind but someday in LSI chip).
...
>	Does anyone have already got this kind of machine ? 
>
>/*******************************************************************************
>    Toshio Nishigaki (E-mail : e50214@kuduts.kudpc.kypto-u.ac.jp)
>    Division of Theoretical Chemistry, Department of Chemistry,
>    Faculty of science, Kyoto Univ, JAPAN
>*******************************************************************************/


This sounds very similar to the problem of building a special purpose
computer for predicting the stability of the planetary orbits in our
solar system.  A computer called the Digital Orrery was built to do
this, and it was used to predict the orbit of Pluto hundreds of
millions of years into the future, in order to find out if the orbit
was stable or not.  The computer was built using 1980 technology and
was about 1 cubic foot in size, used 150 watts, but was 60 times
faster than a VAX 11/780 and 1/3 the speed of a Cray 1 FOR THE
SPECIFIC PROBLEM it was designed to solve.  I've read that it was
designed and built by six people working part-time for nine months,
and it was relatively low cost compared to the alternatives, such as
using a supercomputer.  The calculation of several hundred million
years of Pluto's orbit (to high precision) required the Orrery to run
continuously for five months.

There is a brief discussion of the use of specialized computers for
numerical modelling on page 553 of vol. 32, Number 5, May 1989
Communications of the ACM.  A reference that article gives for the
Digital Orrery is IEEE Trans. Comp. C-34, 9 (Sept. 1985), pp. 822-831.
This work was done by a group of people at MIT, and they wrote the two
references I've given.

Duke