RE: AMBER: problem with protein minimization

From: Ross Walker <>
Date: Tue, 22 Feb 2005 08:47:56 -0800

Dear Yen,

> 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.

This is typically a compiler limit and as far as I can tell there is not
much you can do. You could try reducing some of the other parameters such as
Max real as these probably do not need to be as large as you have them and
may allow you to make max istack bigger, or try a different compiler.
Typically I have found Intel's ifort allows larger static arrays than g77.
Unfortunately there is no easy way to dynamically adjust these values. This
is a left over from the days of Fortran 77 which didn't support dynamic
memory allocation.

Note: Amber8 sander is now Fortran 90 and uses dynamic memory allocation in
place of static sizes.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Feb 22 2005 - 16:53:02 PST
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