Re: [AMBER-Developers] mmpbsa tests (perl and python)

From: MengJuei Hsieh <>
Date: Tue, 30 Mar 2010 21:54:07 -0700

By the way, test.mmmpbsa_py/test.mm_pbsa do run on my laptop without crash,
so I am guessing that fillratio might not be the problem at all.

My simple profiling of sander in these two tests tells me that the largest
virtual size were 6G but largest used memory size was 1G. We might need to
dig more to see what situation prevents it from allocating the memory.

Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
> From: case <>
> Reply-To: AMBER Developers Mailing List <>
> Date: Tue, 30 Mar 2010 14:34:49 -0400
> To: AMBER Developers Mailing List <>
> Subject: Re: [AMBER-Developers] mmpbsa tests (perl and python)
> On Tue, Mar 30, 2010, Jason Swails wrote:
>>> The mm-pbsa test seems to need a lot of memory (1.2 Gbyte or so).  Does
>>> this seem correct to others?  It won't run on my laptop -- is there any easy
>>> way to reduce the size requirement?
>> I think this has to do with istrng in PBSA.  For the mm-pbsa tests (if
>> you're talking about that use a non-zero ionic strength,
>> perhaps try changing it to zero and running again to see if it
>> changes?  Perhaps it will help narrow down this problem.  I gave some
>> files to Mengjuei to look at in regards to this.
> I don't know either mmpbsa script, nor have time to learn right now.  So, if
> anyone can pitch in with changes, I would appreciate it.  FWIW, I get very
> similar errors running the python mmpbsa test case: sander tries to malloc
> about 1.2 Gbytes of memory and fails on my laptop.
> ...thx...dac
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Received on Tue Mar 30 2010 - 22:00:03 PDT
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