AMBER Archive (2002)

Subject: Re: question about nmode again.

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 17 2002 - 09:40:00 CDT

On Tue, Sep 17, 2002, Yongjun Jiang wrote:
>
> Otherwise, if nmode is alone compiled with 64 bit, and it worked well for
> less than 2800 residues. More than 2800 residues, the output file of nmode
> is empty, and a core file is birthed. Of course, the parameters such as
> MAXMEMX, MAXATOM are proper for more than 2800 ones.
>

2800 residues is an enormous number, probably about a factor of 5 larger
than the biggest calculations I have ever done. Since the memory goes like
N**2 and the time like N**3, you are asking to carry out a calculation that
is 25 -125 times larger than what we already consider "big" calculations.
To do this, you are going to have to become an "expert", and probably modify
the code in major ways. Then people can send questions to you, rather than
the other way around.

(It might be worth mentioning that, in 1982 when the code was first written,
I put in a limit of 300 *atoms*, thinking that no one would have the resources
to do anything larger than that....)

..dac 

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