Dear Simon and Jason,
Thank you for your comments and suggestions. I do not know how to use
different random seeds yet, but I will look into it.
I do not know the shaw group either.
Wu
-----Original Message-----
From: Simon Becker [mailto:simon.becker.uni-konstanz.de]
Sent: Wednesday, September 07, 2011 4:59 AM
To: AMBER Mailing List
Subject: Re: [AMBER] results from independent simulations
Am 07.09.2011 11:17, schrieb Jason Swails:
>
> On Sep 6, 2011, at 8:37 PM, "Wu Xu"<wxx6941.louisiana.edu> wrote:
>
>> Dear Amber developers and users,
>>
>>
>>
>> I am doing MD simulation on three structures. The initial structures
are
>> from pdb files, which are 1KBH, 2C52 and 2KKJ.
>>
>>
>>
>> I performed 1-step minimization, 7-step of heating and 50-ns
equilibration
>> (5 ns each equilibration) by following the tutorial B3 using Amber 11
(2
>> nodes and 8 processors/node for equilibration).
>>
>>
>>
>> And then, I independently repeated the exact simulation procedure.
>>
>>
>>
>> Two structures with the lowest energy of 2C52 from the first run and
>> second run are identical. I also obtained the identical structures with
>> the lowest energy for 2KKJ. In contrast, two runs of 1KBH give me two
>> different structures.
>>
>>
>>
>> My question, should we expect the identical results for two independent
>> simulation with the same procedure?
> No. Simulations are chaotic and a protein's accessible phase space is
far too large to be completely sampled by a simulation on the time scales
even of the DE Shaw group.
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.wu: the chaotic nature of md simulation wich jason stated is definitely
true however I have also observed what you described. often the final
structures of identical unrestrained runs, even quite long ones beyond
50ns, were virtually identical; diff"ing the two rst or pdb files
resulted in nothing. You can overcome this using different random seeds
(ig in the cntrl section).
.jason: the shaw group: what are you referring to? is there a
publication I missed (again)? please let me know.
regards
simon
--
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 Universitaet Konstanz
D-78457 Konstanz
mail: simon.becker.uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183
http://strucbio.biologie.uni-konstanz.de/
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Received on Wed Sep 07 2011 - 09:00:02 PDT
