Re: AMBER: problem with protein minimization

From: Robert Duke <>
Date: Tue, 22 Feb 2005 12:10:51 -0500

Yen -
If you have a "default" explicit solvent simulation, pmemd works in a
relatively small memory footprint, and does dynamic memory allocation. It
is available to amber 6/7 licensees as pmemd 3.1 (see amber web page) and is
included as part of amber 8. There are none of these sizing issues with
pmemd. If you are doing something pmemd can't handle, my apologies to
everyone for the noise (I missed the original posting).
Regards - Bob Duke

----- Original Message -----
From: "Ross Walker" <>
To: <>
Sent: Tuesday, February 22, 2005 11:47 AM
Subject: RE: AMBER: problem with protein minimization

> 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
> Ross
> /\
> \/
> |\oss Walker
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
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Received on Tue Feb 22 2005 - 17:53:00 PST
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