Stefan Hoorman wrote:
Hello. Finally came back with the results. Let me again remind you of
what we were talking about. I wanted to obtain the PMF pulling my ligand
out of the protein using umbrella sampling and WHAM. After several
recomendations you asked me to try and simulate the pulling in a one
coordinate fashion. So I have again re-equilibrated my system in such a
configuration so that the pulling now is made only in the Y axis. Here
is what came as a profile this time.
"http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg";
Does this look "normal"? I am a bit worried since I have never worked
with this kind of calculation. The histogram looks fine, well spaced
overlaps between simulations.
Thank you.
I would try to pull further than the distance you have. It appears that the
curve is only just starting to (maybe) level off. You might have a look into
the literature to see if anyone has done the same sort of thing on similar
systems to get an idea of the total pull distance and the shape of the curve.
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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![http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg"](http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg"){kind=link}