On Tue, Mar 30, 2010 at 4:07 PM, Ray Luo <ray.luo.uci.edu> wrote:
> 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.
I set fillratio to 2.0 and I did not see any appreciable change.
istrng is still the variable that will make/break the timing described
previously
>
> 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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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 30 2010 - 14:00:02 PDT
