i don't know that much about pca, but i found the following links that may
be of help:
http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/
http://www.biomachina.org/courses/modeling/071.pdf
cheers!
et
On 27 February 2012 12:03, Carlos Simmerling <carlos.simmerling.gmail.com>wrote:
> it really depends on what you are simulating. "converged" is really a
> measure of the precision of your data- and it depends what the data are.
> How you measure convergence of properties of a folded protein and protein
> folding is very different (though in principle, "converged" for any
> simulation means the same thing, in practice you probably don't mean that).
>
> On Mon, Feb 27, 2012 at 2:08 AM, Catein Catherine <askamber23.hotmail.com
> >wrote:
>
> >
> > Dear Amber Experts,
> > In order to test if the molecular dynamics simulations has converged or
> > not. Hess has suggested to study the cosine content of the principal
> > components. (Physical Review E, Vol. 65, 031910, Convergence of sampling
> > in protein simulations, Berk Hess).
> > Is it possible to be done by AMBER's tools? If yes, could you some hints
> > how to do so? If not, what other tools should we use to get this
> > information? Many thanks.
> > Best regards,
> > Catherine
> >
> >
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Received on Thu Mar 22 2012 - 00:30:02 PDT
