Stefan Hoorman wrote:
> I have included in my simulation some windows past the ~2nm distance
> between the two groups. The same result occurred, but with a longer
> separation, the graphic seems to continue rising and the
histogram looks
> even taller. Here are the links for the profile.xvg,
histogram.xvg and
> the rapidshare link for my histogram.xvg file in case you want to
have a
> look.
> histogram link >
>
"http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg";
> profile link >
>
"http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg";
> histogram text file >
"http://rapidshare.com/files/286236452/histo.xvg.html";
> The histogram file looks like a diagonal matrix of 200X20, in
which the
> "diagonal" range is of approximately 10 lines, i.e., the first
collumn
> has 10 lines of non-zero entries and then 190 of zeros, the second
> collumn has 12 lines of non-zeros, the third has the first three
lines
> of zero entries and then 10 or 12 lines of non-zeros and then lots of
> zeros again, and so on and so forth.
Right, there are multiple datasets in the histo.xvg file. However
you're
plotting it (i.e., the image linked above) is not correct. See here
for a
proper look at your histograms:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Images/Gromacs/histo_sh.jpg
I suppose the histograms look good; I don't see anything
horrendously wrong that
would give weird behavior.
Do you have sufficient space in your box to do this pulling? Could
you be
running into periodicity effects? Have you tried doing a 1-D pull
instead of
pulling in two dimensions, as I suggested before?
-Justin
Now you mentioned it, I do in fact have periodicity effects in some of
the pull windows. I will try to set the system in a larger box and
That probably explains it. The distance you pull needs to be less than half the
box length in the direction you're pulling.
orient groups in a way so that I can do the 1D pulling. Should have the
results in a few days. In the mean time, did you use xmgrace to plot the
histogram? How did you get such a nice histogram graph?
Yes, use:
xmgrace -nxy histo.xvg
-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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![http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg"](http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg"){kind=link}
![http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg"](http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg"){kind=link}
