[gmx-users] PMF curve

Justin A. Lemkul jalemkul at vt.edu
Mon May 30 17:12:46 CEST 2011

mohsen ramezanpour wrote:
> Thank you.
> no,I think the problem is not zero point.
> Actually I maean some thing like this one.please have a look at new 
> attached file.
> I just added 3 new windows in 0.3 - 0.8
> But the whoe of my curve shifted upward.
> There is another question:
> Actually I pulled my drug from 0.18 - 3.18
> then,extracted some windows.umbrella0 for 0.18 and umbrella20 for 3.18
> Besides as we know drug is oscilating in it's windows.
> so ,it must cover places as like as 0.12 and 3.22 too.
> Am I right?

Possibly.  Harmonic potentials allow for oscillation.  The amount by which the 
position shifts is a function of both the force constant you apply and the 
nature of the interactions within the system.

> But looking at curve it seems my drug couln't cover the region around 0.18
> besides it ha covered completely(untill 0.03) the region around 0.18
> What is the problem?
> Since I started from 0.18 (which energy is negative there),I am in doubt 
> about starting point.
> Because it can be eighter 0.03 OR 0.18

All of this appears to be a consequence of poor sampling.  You have several flat 
locations in both the PMF curves, indicating absolutely no sampling in that 
region.  Your histograms should show you this, as well.  You need more windows 
and more time in each.  Based on what you've shown, your simulations are simply 



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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