Hi Thomas,
thank you for your reply.
Hi Mike,
Your confusion might stem from a very simple issue.
To see the overlap of the forward and backward distributions,
you have to plot
N(+Delta H(lambda=x) | lambda=y) and
N(-Delta H(lambda=y) | lambda=x).
Do I understand it right, that for instance (consider lambda step = 0.5)
ONLY
N(+Delta H(lambda=0) | lambda=0.5) AND N(-Delta H(lambda=0.5) |
lambda=0)
has to overlap, and then
N(+Delta H(lambda=0.5) | lambda=1) AND N(-Delta H(lambda=1) |
lambda=0.5)
has to overlap, to get an accurate estimation of the free energy
difference, and not (essentially) other distributions? An example would
really help me out of my confusion :(
That is, you have to plot the histogram for the negative of the energy
difference samples in the backward direction.
And is it right, that N(-Delta H(lambda=y) | lambda=x) equals N(+Delta
H(lambda=y) | lambda=x) if I
simply mirror the distribution at the y-axis?
See also the original paper of Charles Bennett for an explanation of
the overlap and how it is measured.
I read the original paper a couple of times, and I understand, that the
squared value of the standard deviation (eq 11) measures the overlap.
And according to Fig.5, I understand, that the (complementary) fermi
functions have to show an overlap and that in principle the method
calculates the perturbation between A -> B via a shifted state by a
constant C in between. But I cannot bring it to the context of the g_bar
output
N( Delta H(lambda=x) | lambda=y).
How are the fermi functions and the constant C related to N( Delta
H(lambda=x) | lambda=y) in detail?
Or did I miss the definition in Bennett's paper, where is said, which
distributions in detail have to overlap and how they are defined?
Best,
Thomas.
---------------------------------------------------------------------------------
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
---------------------------------------------------------------------------------
Thank you for any help,
Mike
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