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

From: Ray Luo <>
Date: Tue, 30 Mar 2010 13:07:30 -0700

The large memory usage is probably due to the fact that both scripts are
setting fillratio = 4 right now so the grid setting error will never get
triggered. This leads to a grid too large except for small organic

MJ is in the process of making the grid setting routine more
intelligent. The routine will try to use a larger fillratio if the
current fillratio is too small. This will be done successively until a
large enough fillratio is found. This is a minor enhancement and can be
done today.

All the best,

Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: Phones: (949) 824-9528, 9562

case wrote:
> 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 - 13:30:03 PDT
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