<br><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;">
Stefan Hoorman wrote:<br>
><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<br>
> histogram looks<br>
> > even taller. Here are the links for the profile.xvg,<br>
> histogram.xvg and<br>
> > the rapidshare link for my histogram.xvg file in case you want to<br>
> have a<br>
> > look.<br>
> > histogram link ><br>
> ><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>
> ><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 ><br>
> "<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<br>
> which the<br>
> > "diagonal" range is of approximately 10 lines, i.e., the first<br>
> 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<br>
> 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<br>
> you're<br>
> plotting it (i.e., the image linked above) is not correct. See here<br>
> 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<br>
> horrendously wrong that<br>
> would give weird behavior.<br>
><br>
> Do you have sufficient space in your box to do this pulling? Could<br>
> you be<br>
> running into periodicity effects? Have you tried doing a 1-D pull<br>
> instead of<br>
> pulling in two dimensions, as I suggested before?<br>
><br>
> -Justin<br>
><br>
><br>
><br>
> Now you mentioned it, I do in fact have periodicity effects in some of<br>
> the pull windows. I will try to set the system in a larger box and<br>
<br>
That probably explains it. The distance you pull needs to be less than half the<br>
box length in the direction you're pulling.<br>
<br>
> orient groups in a way so that I can do the 1D pulling. Should have the<br>
> results in a few days. In the mean time, did you use xmgrace to plot the<br>
> histogram? How did you get such a nice histogram graph?<br>
<br>
Yes, use:<br>
<br>
xmgrace -nxy histo.xvg<br>
<br>
-Justin<br>
<br></blockquote></div><br>Hello. Finally came back with the results. Let me again remind you of what we were talking about. I wanted to obtain the PMF pulling my ligand out of the protein using umbrella sampling and WHAM. After several recomendations you asked me to try and simulate the pulling in a one coordinate fashion. So I have again re-equilibrated my system in such a configuration so that the pulling now is made only in the Y axis. Here is what came as a profile this time. "<a href="http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg">http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg</a>"<br>
Does this look "normal"? I am a bit worried since I have never worked with this kind of calculation. The histogram looks fine, well spaced overlaps between simulations.<br>Thank you.<br><div id="DirectContainer" class="contianerCopyCodeCtrl">
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