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
molecules.
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
==========================================
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: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
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 mm_pbsa.pl) 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
