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 Mon Feb 27 2012 - 04:30:02 PST
