On Tue, Mar 30, 2010 at 2:34 PM, case <case.biomaps.rutgers.edu> 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.
In the test directory for mmpsba_py, edit the mmpbsa.in (printed
within Run) to say istrng=0 instead of istrng=0.1. This will
certainly make the numbers different, but do you still get the
outrageous memory requirements?
>
> ...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 - 13:00:03 PDT
