RE: size of a simulation system

From: Kristina Furse <>
Date: Tue, 1 Apr 2003 16:36:01 -0600

Hi Wen-

I am currently running a periodic simulation on 104234 atoms (water box) using
Amber7. Using 16 processors on an SGI origin I get ~2.4ps/hr. (I ran into
diminishing returns in time gain, so there was no point in running on more
than 16 proc.) Even with the generous assumption that your system would only
run 7 times slower, my estimation says ~608 days to get 5ns, so you're looking
at ~20 months at the very least.

Good luck,


>===== Original Message From =====
>On Tue, Apr 01, 2003, Wen Li wrote:
>> I am planning to run an MD simulation using Amber7 on a system of an
>> RNA-RNA complex including a total of 170 nts. With a water box, the
>> system includes a total of 721918 atoms. Is it practical to run a 5 ns MD
>> simulation on such a big system?
>As far as I know, this would be a bigger simulation (by quite a bit) than
>anybody has run so far. Are you sure that you cannot look at a smaller
>piece of your system? I would recommend getting really comfortable running
>and analyzing a system with maybe 5% this number of atoms (say 30,000 or
>so); then figure your execution times to be at least 20 times longer for
>the bigger system.
>This is almost a case of, "if you have to ask, you can't afford it".
>David A. Case | e-mail:
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA |

Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Received on Tue Apr 01 2003 - 23:53:00 PST
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