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

[Stefan Hoorman]

>
>
> > To generate each window I use "trjconv -f
> > original_separation_trajectory.xtc -s topol.tpr -dump
> > time_where_specific_distance_is_found -o
> > frame_where_separation_between_structures_is_x.gro"
> > Once I have the coordinate files regarding this specific distance
> > between my pull groups, I simulate each of them (using the same
> > topol.top file, index.ndx...etc) but with the new md_pull.mdp file I've
> > shown here earlier.
> > Is this wrong for wham analysis?
>
> This should be right, hence my confusion about the histogram.  Are you sure
> there's only one peak?  Have you looked at it with a text editor?  There
> should
> be multiple entries in the file, one for each window that you're
> simulating?
>
> -Justin
>
> > Thank you
>

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.
In case you prefer another way for me to show you the histogram text file,
please let me know.
Thank you
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