[gmx-users] starting conformation different

[Tsjerk Wassenaar]

Hi Priya,

Consider the following:
You've put one person in the Himalaya, one in Delhi and one in Bombay,
you let them walk for a month each, and you wonder why they don't end
up in the same place, asking which place it is you should consider
correct then. Pretty absurd, but exactly what you're asking.

The thing is, there is no one correct structure; the only thing is the
ensemble. Running for a longer time should lead to convergence in the
sampling of each of your simulations, but by no means in equal end
structures.

Hope it helps and best wishes for 2007

Tsjerk

On 12/27/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> priya priya wrote:
> > Dear All
> >
> > If i start MD with different geometries for the same peptide fragment,
> > ie. different conformation (phi,psi angles)..........and run the
> > simulations for 5ns on all the conformations.....i get different results
> > from all the fragments simulated in vacuum.
>
> This is a bit like baking bread either with egg or with no egg and
> varying the amount of flour each time. The flour will cause minor
> variation and the egg content will make for a result that does not
> resemble the alternative...
>
> > Please suggest me the criteria for selecting the appropriate structure
> > from all the final conformations obtained.
>
> Unfortunately that's your job, and it depends what you intended the
> exercise to produce.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623