[gmx-users] New tutorial available - umbrella sampling

Jochen Hub jochen at xray.bmc.uu.se
Mon Jan 25 11:22:24 CET 2010

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 ...

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,


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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