AMBER Archive (2005)

Subject: Re: AMBER: problem with protein minimization

From: yen li (chem_me2000_at_yahoo.com)
Date: Tue Feb 22 2005 - 03:26:37 CST

Dear Sir,
I tried increasing the MAX_ISTACK value in sizes.h and
the numbers in the error message also changed. but as
i increase the value of MAX_ISTACK beyond 30000000 and
MAXINT beyond 50000000, there is segmentation fault in
the sander. Is there some limit set for these
parameters in amber7. I also want to know that whether
there is a way in which memory can be allocated
dynamically.
Thanks

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Mon, Feb 21, 2005, yen li wrote:
>
> > but with the straight chain, it gives error
> > for some of the parameters of sizes.h header file.
> The
> > output file is given below. I also tried changing
> the
> > indicated parameters and then recompiling, but it
> > didnt help.
>
> Did the numbers in the error message change when you
> increased MAX_ISTACK?
> (They should, especially that lastist value).
> Sometimes you have to keep
> increasing this value until the program is happy.
>
> >
> > Exceeding lastist in get_istack
> > lastist = 30000000
> > top_stk= 21868392
> > isize = 21027300
> > request= 42895692
> > Increase MAX_ISTACK in sizes.h and recompile
>
> Sander is not written efficiently for doing a
> simulation of a very long
> straight chain. Mike Crowley might give you a
> better idea of what is going
> on, but don't give up too soon on increasing
> MAX_ISTACK.
>
> ...dac
>
>
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