Hi Justin,
I think you did a great job with that tutorial, a lot of people will
benefit from it. I have just 2 additional suggestions:
1) Maybe you can comment on the issue of equilibration, especially since
you took your initial frames from a non-equilibrium pulling. In such
cases you probably want to play with the -b option of g_wham an generate
a series of PMFs with different equilibration times, such as
for b in 100 200 300 400 ... ; do
g_wham -b $b -o prof.b$b -hist hist.b$b ...
done
and compare the profiles. This way one can check how long you need to
equilibrate. As long as the PMF changes with b you may have an
equilibration issue.
2) Concerning the histogram plot. That is actually a good example where
one needs more umbrella windows since there is hardly any overlap
between some of the histograms, between green and blue for instance.
Maybe you can point that out in the tutorial.
But hey, great job,
Jochen
Justin A. Lemkul wrote:
Hi all,
I've been working on an umbrella sampling/PMF tutorial for some time
now, and I have just added it to the Tutorials page on the Gromacs
site. As with my previous tutorials, I would welcome anyone to look
through it and give me any feedback you may have on making it better;
feel free to email me on-list or off.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
Since use of the pull code seems to be a common inquiry across the
list, I hope this instructional material will help out.
-Justin
--
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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