On 2012-04-01 20:05, Ignacio Fernández Galván wrote:
--- On Sun, 1/4/12, David van der Spoel<[email protected]> wrote:
It depends what you want to compare to.
Fair enough. For the moment I don't want to compare to anything. I just want to
extract a number of uncorrelated configurations from the simulation, and to
know what's the minimum interval at which I should sample configurations.
Something like what's explained in pp. 164-ff of this book:
http://books.google.es/books?id=GT9oPnAEkEQC
The relaxation time of a
velocity averaged per atom can be analyze by fitting the vac
to y = exp(-t/tau). This gives 5 fs in your graph.
5 fs? Don't you mean 5 ps? In that case, how do arrive to such value? It can't
be a simple exponential fit, because the function is oscillating. Do you just
guess it by the way the amplitude shrinks?
This is my main problem, I don't see how one can fit an exponential to an
oscillating function.
Of course you can, but what does it mean?
Indeed if I take the absolute value of the function I get 150 fs.
No time to read your book, but I think the data is fine.
Thank you,
Ignacio
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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