Re: different seeds and protein behavior

From: Aron Broom (
Date: Fri Jul 20 2012 - 11:58:13 CDT

yes I did mean free energy. Indeed it will switch if given long enough,
but for a process like protein folding, that might mean a simulation that
covers several seconds...

On Fri, Jul 20, 2012 at 10:06 AM, Ajasja Ljubetič <
> wrote:

> 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,
> Ajasja

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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