On Mon, Aug 12, 2002, William Wei wrote:
> Hi, Amber funs, I run parallel sander on Onyx. A 16 processors and 8
> processors parallel jobs and two other one processor minimization. They cost
> about 28G swap, but only 3.0 G memory. In my computer I have totally 35G
> memory, I want to use more of them to speed up my dynamics simulation. Can
> anyone give ma a suggestion for how to modify the source file(s), and how
> much memory should I create for the sander? Thanks, and have a good day.
>
Except on really gigantic systems, Amber doesn't require very much memory.
Memory usage is printed out near the beginning of sander runs. Reals take
8 bytes, integers 4 (on most machines, i.e. unless you compiled with -64
on the Onyx.)
>From the distribution:
DHFR + water (23000 atoms): about 45 Mbytes
rt_polymerase (141000 atoms): about 300 Mbytes
These are for a single processor; values will be somewhat smaller for
parallel jobs.
If we knew of any code modifications to make that would speed up simulations,
we would have already put them in :-)
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
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 | http://www.scripps.edu/case
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Received on Mon Aug 12 2002 - 08:55:55 PDT
