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

[Stefan Hoorman]

> 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 >
> >      >
> >     "
> 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
>
> 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
>
> -Justin
>
>
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. "http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg"
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.
Thank you.
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