[gmx-users] COsine content of ED analysis

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Tue Sep 7 10:09:47 CEST 2004

> The problem is that there is not one potential well, but there are many.
> On a timescale of 5-10ns you might sample only one well.
> But on longer timescales you will see jumping between many of these
> wells. See for instance:
> Hess, B. Convergence of sampling in protein simulations. Phys. Rev. E
> 65:031910, 2002.
> Berk.

that may be, but even while walking in the first "well" the flexibility
required to jump to the next wells is already available - it is simply
embedded/described by the fold that the protein is in. In addition there
are significant overlaps between ED eigenvectors calculated from clusters
of crystal structures or NMR ensembles (i.e. real experimental data). So
perhaps it is not totally useless to use simulation times of less than 10


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