[gmx-users] COsine content of ED analysis
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Tue Sep 7 10:32:48 CEST 2004
> I agree.
> Often prolonging a simulation will only results in (a small) extension
> of the sampling in the directions that have already been sampled before.
> But you can never be sure that the protein might do something different
> when you sample even longer.
> Note that at very long timescales it also becomes questionable if the
> are accurate enough.
I completely agree on the force field point - despite many people's best
efforts over the past 3 decades the FFs are not good enough for long
simulations - and (at the risk of starting a flame war) many papers
reporting on "unfolding" proteins with simulations may have been looking
more at forcefield instability rather than "true" unfolding pathways.
Back to the cosine content: all cows are beasts but not all beasts are
cows - translated: a sign of too short sampling is correlated with a high
CC content, but is it not possible there are "true" motions with a high CC
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