AMBER Archive (2003)

Subject: memory shortage with mm_pbsa

From: Peter Anderson (toutvabien78_at_yahoo.com)
Date: Tue Jul 08 2003 - 19:36:09 CDT

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 mm_pbsa.pl 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
processors?

Thank you very much,
Peter Anderson

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