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

[Justin A. Lemkul]

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

> Thank you
>  
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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