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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 30 Mar 2010 12:02:36 -0400

Hi Mengjuei,

I've attached a tarball with the appropriate files and a script with
the sander call used. On my machine, this takes around 8 minutes (2.4
GHz core 2 quad, 8 GB of RAM). Changing istrng to 0 drops the time
required to 46 seconds.

Thanks!
Jason

On Mon, Mar 29, 2010 at 8:57 PM, Mengjuei Hsieh <mengjueh.uci.edu> wrote:
> On Mon, Mar 29, 2010 at 07:13:49PM -0400, Jason Swails wrote:
>> As an update to this, I'm finding some weird timings with PB when run
>> through our script.  Below is the input file being printed by our
>> script, so maybe someone more familiar with PBSA can enlighten me as
>> to which variables I am setting that is killing the performance.
>>  Here is the input file:
> [snipped]
>> When istrng is set to 0, this will finish 1 frame in 1.613 minutes.
>> When istrng is 100.0 (mM), 1 frame takes 20.057 minutes (I'm not sure
>> which revision this started happening in, but it's relatively recent).
>
> Hi, this sounds very interesting and we are intrigued by this
> kind of performance difference. Can you send me a test case
> so that I can reproduce the problem? I'll tehn report to recent
> PBSA revision contributors.
>
> Regards,
> --
> Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
> University of California Irvine.
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
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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 - 09:30:03 PDT
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