memory shortage with mm_pbsa

From: Peter Anderson <>
Date: Tue, 8 Jul 2003 17:36:09 -0700 (PDT)

Dear Amber Users,

I am trying to perform an entropy calculation using
the mm_pbsa command and I'm encountering memory
problems. I enter the command, some
calculations with sander work fine for about a minute,
and then an nmode calculation begins and quickly
fails. The bottom of the resulting "nmode_lig.1.out"
file reads:

Total memory required : 15425318 real words

Total memory avail : 3500000 real words

Total memory required : 71522 integer words

Total memory avail : 4000000 integer words

Maximum nonbond pairs 3928477
increase the real memory by 11925318 words

I assume that the mm_pbsa's limitation to a single cpu
(am I correct?) is the root of this memory shortage.
Does anyone know how I can get around this memory
problem? Can I spread the job out onto multiple

Thank you very much,
Peter Anderson

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Received on Wed Jul 09 2003 - 01:53:00 PDT
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