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

From: Jason Swails <>
Date: Tue, 30 Mar 2010 15:43:31 -0400

On Tue, Mar 30, 2010 at 2:34 PM, 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.

In the test directory for mmpsba_py, edit the (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
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Tue Mar 30 2010 - 13:00:03 PDT
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