AMBER: Re: memory shortage with mm_pbsa - some more thoughts

From: Qing Zhang <>
Date: Mon, 14 Jul 2003 16:10:26 -0700 (PDT)

--- Joffre Heredia <> wrote:
> .....
> This should not be a problem with the actual cheap
> prices of memory, but
> the main problem we are having is that our compiler
> (SGI Fortran 90
> compiler) does not allow to STATICALLY allocate more
> than 258 MB of
> memory. This way, even with a great amount of memory
> available, we are
> not allowed to compile Nmode to use more than about
> 2.000 or 2.500 atoms.

Hi, I met the exactly the same problem when dealing
with a system of 4,000 atoms. But this memory
limitation on Fortran compiler can be solved by
compiling AMBER at 64 bits instead of 32 bits. (AMBER
has to be uninstalled completely at first because many
modules including Nmode share the same library
compiled at 32 bits, then reinstall AMBER at 64 bits.)

BTW, compilation of AMBER at 64 bits can also make CG
minimization possible converge to low gradients, such
as 10^(-4), which is usually required by Nmode for
calculating entropy. (I use AMBER 7.)

Good lucks,

Qing Zhang
Department of Chemistry
New York University

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Received on Tue Jul 15 2003 - 00:53:01 PDT
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