Re: different seeds and protein behavior

From: Ajasja Ljubetič (
Date: Fri Jul 20 2012 - 09:06:58 CDT

On 20 July 2012 15:50, Aron Broom <> wrote:

> certainly you can do have two different dynamic behaviors. In protein
> folding these would be considered parallel pathways. Similarly you can
> even have two different, but well converged end-states in the event
> (although perhaps not that likely) that the free-energy landscape for your
> process has two equally deep global mimima, or two equally deep local
> mimima within the region you are interested in.
> Yes, but I have a feeling ergodicity is always assumed in MD. So if we
make that assumption, then during a long enough simulation your system
should switch between all accessible states.

 It all just comes down to energy in the end.

Well I agree if you mean free energy. (So in other words, entropy
is important as well)

Best regards,

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