On Fri, Sep 02, 2005, Ananda Rama Krishnan Selvaraj wrote:
> i have tried to do the MD simulation of organic
> molcules (about 14592 atoms). i am got the following error..
>
>
>
>
> -------------------------------------------------------
> Amber 7 SANDER Scripps/UCSF 2002
> -------------------------------------------------------
>
> Static Integer Memory requirement of:13815257 exceeds MAXINT of
> 2000000
>
> | Memory Use Allocated Used
> | Real 2000000 1071496
> | Hollerith 400000 87682
> | Integer 2000000 13815257
>
> | Max Nonbonded Pairs: 5400000
> ** Redimension and recompile
You normally have to edit sizes.h to increase MAXINT and re-compile. But
something seems amiss with your setup, since 14,000 atoms should not require
so much memory. Take a look at the test cases in $AMBERHOME/test/dhfr (for
example), and see if you are doing anything different. (I'm assuming that
all of the test cases run OK for you.)
I would certainly recommend trying a non-MPI calculation first, before running
a parallel simulation (again: assuming that you have not already done this.)
....good luck...dac
--
==================================================================
David A. Case | e-mail: case.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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Sep 02 2005 - 17:53:00 PDT
