On Thu, Sep 28, 2000, schayg_at_puskin-a206.sote.hu wrote:
> I am trying a normal mode calculation on a protein with 320 residues.
>
> Total memory required : 129902965 real words
In this case, a "real word" holds a double precision varaible = 8 bytes.
Hence, you need a little over 1 Gbyte of memory to run this job.
Here's why: 320 residues is probably something like 5000 atoms, which means
3*5000 = 15000 x,y,z coordinates. To hold the second derivative matrix,
you would need 15000*15000/2 = 112000000 double precision numbers, or
about 1 Gb of memory just for that part.
> i am trying to run this on a Linux box with 64M memory and 130M virtual
This is unfortunately not really a feasible calculation for this platform.
Very different algorithms (probably taking advantage of sparse matrix
techniques) would be required for such a calculation.
>
> i am also wondering about the available memory it reported, it seems very
> low...
This is set in sizes.h, which has more explanation about these things.
...hope this helps...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
==================================================================
Received on Thu Sep 28 2000 - 08:09:53 PDT
