[gmx-users] Re: Re: Re: Re: Re: Re: Re: Re: umbrella potential
stefhoor at gmail.com
Thu Oct 8 17:58:12 CEST 2009
> Stefan Hoorman wrote:
> > > I have included in my simulation some windows past the ~2nm
> > > between the two groups. The same result occurred, but with a
> > > 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 >
> > "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
> > > 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:
> > 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
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
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
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