[Beowulf] Intro question

Bogdan Costescu Bogdan.Costescu at iwr.uni-heidelberg.de
Mon Dec 8 06:11:04 PST 2008

On Fri, 5 Dec 2008, Lux, James P wrote:

> Now consider using that nifty compchem box to go examine thousands 
> of possible drugs.

I don't think that this is the main purpose of the DEShaw machine. 
Thousands of independent trials can be done today with thousands of 
machines: f.e. one trial per machine, much like Monte Carlo 
calculations. Machines like the DEShaw one are useful in 2 cases:
- simulating a much larger system, getting to the point of simulating 
whole cells or at least mitochondria
- simulating a much longer period of simulated time in the same real 
time, as processes of biological interest happen on timescales that 
are many orders of magnitude larger than what can be currently simulated.

In each of these cases there is only one simulation running - a very 
fine grained one...

Bogdan Costescu

IWR, University of Heidelberg, INF 368, D-69120 Heidelberg, Germany
Phone: +49 6221 54 8240, Fax: +49 6221 54 8850
E-mail: bogdan.costescu at iwr.uni-heidelberg.de

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