Re: memory allocation in mm_pbsa

From: James W. Caldwell <>
Date: Wed 11 Sep 2002 08:26:19 -0700 (PDT)

You may have an Operating system limit on how much memory
you can access as sander shouldn't have any problem with
a system of that size. Check with your local IRIX guru
on the configuration of your machine.


On Wed, 11 Sep 2002, Giulio Rastelli wrote:

>Dear all,
>I am using mm_pbsa to post-process a trajectory file made with sander
>using explicit solvent and PBC (about 41000 total atoms). The script
>invokes sander to calculate the
>MM part, but my sistem is too big to get sander working:
> Failed to allocate memory for ipairs: 865675245 (I am using
>This is because the sander input created by mm_pbsa has a cut-off larger
>the system size (99999.0) and there are too many non-bonded pairs.
>I am using a Fuel R14000, 512Mb
>Thank you very much in advance for the reply

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email)
513 Parnassus Avenue                      
University of California                  
San Francisco, CA 94143-0446               
Received on Wed Sep 11 2002 - 08:26:19 PDT
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