[gmx-users] Re: Re: Re: Re: Re: Re: Re: umbrella potential
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 29 14:03:54 CEST 2009
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 >
> > profile link >
> > histogram text file >
> > The histogram file looks like a diagonal matrix of 200X20, in
> which the
> > "diagonal" range is of approximately 10 lines, i.e., the first
> > 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
> > 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
> plotting it (i.e., the image linked above) is not correct. See here
> for a
> proper look at your histograms:
> 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?
> 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?
xmgrace -nxy histo.xvg
> Thank you
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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