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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 28 23:58:53 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 > 
> "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:


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?


> In case you prefer another way for me to show you the histogram text 
> file, please let me know.
> Thank you
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list