mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding to PMF curve which resulted from Umbrella sampling:
I obtained the following curve.
Dose it mean?Because it is not similar to yours in tutorial :(
if yes,please let me know what is the Delta G value approximately?
Because I don't know difference between which points is my Delta G.There
are some points with negative values,
and there are a pick (hill like region ) before being converged at high
values!
Please clarify - is this the result you obtained from running the tutorial? If
this is some other system, I'm not going to try to guess what your result should
look like. The curve is a bit rough, so maybe you need a bit more sampling to
smooth it out, but complex PMF curves are not necessarily wrong. The result
will depend on the interactions your system experiences along the reaction
coordinate. There may be local minima and other metastable states along the way.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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