<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br>
> I have included in my simulation some windows past the ~2nm distance<br>
> between the two groups. The same result occurred, but with a longer<br>
> separation, the graphic seems to continue rising and the histogram looks<br>
> even taller. Here are the links for the profile.xvg, histogram.xvg and<br>
> the rapidshare link for my histogram.xvg file in case you want to have a<br>
> look.<br>
> histogram link ><br>
> "<a href="http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg" target="_blank">http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg</a>"<br>
> profile link ><br>
> "<a href="http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg" target="_blank">http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg</a>"<br>
> histogram text file > "<a href="http://rapidshare.com/files/286236452/histo.xvg.html" target="_blank">http://rapidshare.com/files/286236452/histo.xvg.html</a>"<br>
> The histogram file looks like a diagonal matrix of 200X20, in which the<br>
> "diagonal" range is of approximately 10 lines, i.e., the first collumn<br>
> has 10 lines of non-zero entries and then 190 of zeros, the second<br>
> collumn has 12 lines of non-zeros, the third has the first three lines<br>
> of zero entries and then 10 or 12 lines of non-zeros and then lots of<br>
> zeros again, and so on and so forth.<br>
<br>
Right, there are multiple datasets in the histo.xvg file. However you're<br>
plotting it (i.e., the image linked above) is not correct. See here for a<br>
proper look at your histograms:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Images/Gromacs/histo_sh.jpg" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Images/Gromacs/histo_sh.jpg</a><br>
<br>
I suppose the histograms look good; I don't see anything horrendously wrong that<br>
would give weird behavior.<br>
<br>
Do you have sufficient space in your box to do this pulling? Could you be<br>
running into periodicity effects? Have you tried doing a 1-D pull instead of<br>
pulling in two dimensions, as I suggested before?<br>
<br>
-Justin<br>
<br>
<br></blockquote><div><br>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 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?<br>
Thank you<br> <br></div></div><br>