Stefan Hoorman wrote:
I simulate 400 ps for each window. I have a total of 20 windows. My
400 ps is relatively short, especially given the speed of current hardware and
of Gromacs 4.0. I generally see longer time periods in the literature.
histogram looks like a chromatographic peak ranging from 0.74 and 0.91
Then you are not getting the separation you described before (>2.5 nm). It
looks like you are only pulling a distance of 0.17 nm total.
in the x axis and the count (y axis) goes up to 30000. Is there a way to
index my histogram.xvg or my profile.xvg file and send it to the gromacs
user's list? Or is it not necessary?
The best way to send this information is to generate image files and post them
to a free site where others can see them (photobucket, etc). Up to you to
determine whether its necessary. At this point, I think you are just not
getting what you think you are setting up.
-Justin
Thank you
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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