[gmx-users] Re: Re: Re: Re: Re: Re: Re: umbrella potential

Stefan Hoorman stefhoor at gmail.com
Tue Sep 29 13:57:32 CEST 2009

> > 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 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?
Thank you
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