On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
overlap. Actually, I did it strictly based on Justin's tutorial, with the
sample spacing of 0.2 nm.
Please note that the exact protocol in the tutorial may or may not be applicable
to all systems. The overall workflow is the same, but details regarding use of
groups, .mdp files, etc may vary.
Here are some lines from the end of the energy file (The energy should not
decrease since it was in summation):
Distance(nm) Energy (Kcal/mol) 5.288348 5.705318e+01 5.316250
4.881724e+01
5.344152 4.022505e+01 5.372054 3.101854e+01 5.399956 2.208200e+01
5.427858
1.343340e+01 5.455761 4.267619e+00 5.483663 -5.084078e+00 ? minus 5.511565
-1.486168e+01 ? minus 5.539467 -2.393515e+01 ? minus 5.567369 -3.343453e+01
? minus
What energetic term is this? A summation can decrease if the values being added
are all negative.
Followings are some lines from the end of histograph file:
Distance(nm) 5.455761 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 8 5.483663 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 8 5.511565 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 12
5.539467 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
4 5.567369 0 0 0 0 0 0 0 0
0 0
0 0 0 0 0 0 0 0 2
I am really depressed because it took me quiet a long time to sampling but it
seems in vain... I really no idea to find out what went wrong.
Nor do we. What is in your .mdp file? How many windows are you using? What is
the total desired length of the reaction coordinate, and what are the initial
and final COM distances that you are restraining? What are your box dimensions?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
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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