[gmx-users] PMF curve

Justin A. Lemkul jalemkul at vt.edu
Mon May 30 16:27:52 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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