AMBER Archive (2004)

Subject: Re: AMBER: memory problem in NMODE

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 19 2004 - 16:54:34 CDT

On Mon, Apr 19, 2004, xhu1_at_memphis.edu wrote:
>
> I am doing normal mode analysis of protein by nmode of amber 7. The
> protein has 198 residues(1520 atoms). I got a memory problem:
>
> >Total memory required : 132758715 real words
> >Total memory avail : 15000000 real words
> >Total memory required : 202865 integer words
> >Total memory avail : 4000000 integer words
>
> >Maximum nonbond pairs 3797134
> >increase the real memory by 117758715 words
>
> I increased the real memory to 140000000 at sizes.h file, and tried
> again. This time I got "Segmentation fault...(core dumped)".

Was there any output? Do smaller problems work on your system?

Check your shell limits (use the "limits" command). You may have to
invoke commands like

limit datasize unlimited
limit memoryuse unlimited

(These are just guesses since you don't say what cpu or operating system
you are using....)

...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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