AMBER Archive (2005)

Subject: Re: AMBER: Error in MD run!

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 02 2005 - 11:27:33 CDT

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_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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