On 1/28/13 9:00 AM, Steven Neumann wrote:
Dear Gmx Users, Dear Justin,
I run umbrella samplig with small molecule binding protein. With 11
windows and 0.2 nm spacing I got:
PMF:
http://speedy.sh/zevcp/profile.JPG
Hisotogram:
http://speedy.sh/8Cua2/histo.JPG
(I used -min and -max options of g_wham so leftmost and rightmost
hisotgrams are cut)
Each window is 100 ns. Could you please advise me why my PMF curve is
not smooth? The result is something I expect but do not understand the
little sharp edges on my plot.
How can I make it smooth?
You can't force your data to fit a preconceived notion of what is aesthetically
pleasing. Look at the value of DeltaG - it's less than 1 kcal/mol. Each of
those fluctuations indicates an extremely small value of energy. I don't see
anything wrong with the results. g_wham has the ability to produce very nice
error estimates; if you have doubts about your convergence or reliability of the
outcome, I suggest you investigate those features.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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