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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Received on Wed Sep 07 2011 - 02:30:02 PDT
