Re: different seeds and protein behavior

From: Aron Broom (
Date: Fri Jul 20 2012 - 08:50:40 CDT

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. It all just comes down to
energy in the end.

On Fri, Jul 20, 2012 at 8:56 AM, Dr. Eddie <> wrote:

> Thanks you all for your input. If I may ask a more specific followup:
> Isn't it entirely possible (if not likely) that a protein can have multiple
> convergent behaviors?
> Say I am interested in the distance between two residue's carbon-alpha's,
> but assume the protein will not denature and is started close to its 0K
> structure. I perform 10 runs and I get two distinct behaviors (one distance
> distribution around 6 Angstroms the other around 8). Which is more likely:
> 1) The protein has two distinct "heated" dynamical behaviors
> or
> 2) I have not run for a sufficient amount of time and I should expect with
> more time each type will "switch" over and in the end I will get the
> average.
> Thanks,
> Eddie
> On Fri, Jul 20, 2012 at 3:14 AM, Nicholas M Glykos <>wrote:
>> What you refer to is the crux of sufficient sampling. If different runs
>> (or different parts of the same run) produce statistically different
>> results, then your measured quantites have not converged (and you should
>> continue the simulation). Although demonstrating sufficient sampling is
>> the name of the game in the field, in some cases (eg folding simulations)
>> there is not a consensus of how to demonstrate it in the first place
>> (eigenvector overlap from dPCA or cPCA is our current favorite, but
>> opinions across the community do vary).
>> My twocents,
>> Nicholas
>> --
>> Nicholas M. Glykos, Department of Molecular Biology
>> and Genetics, Democritus University of Thrace, University Campus,
>> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>> Ext.77620, Tel (lab) +302551030615,
> --
> Eddie

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

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