[gmx-users] PMF curve

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Thank you for your reply
> 
> Actually my system is not the same as tutorial.

Then you should not equate the results, or be concerned when things look 
different.  Every system is different.

> I tried to obtain protein-drug delta G.
> I obtained that.
> Yes,you are right,since I don't have good computaional systems I 
> couldn't run more than 1 ns for each windows.
> 
> when there are some minimum and maximum in our curve ,How do I must 
> evaluate Delta G?
> the difference between minimum and maximum values OR difference between 
> values corresponding to
> 0 and last windows(where they must be converged(be flatted))?

Revisit fundamental thermodynamics.  DeltaG is the difference in free energy 
between the final and initial states.  It doesn't matter how you get there - 
DeltaG is a state function.  Like I said, there may be local maxima or minima 
along the reaction coordinate, but the DeltaG for the process is still the 
highest point (where the PMF has leveled off, presumably in solution) minus the 
energy value at your starting point (your global minimum, it would seem).

> 
> Besides when I add a new windows in places which there are not enough 
> sampling ,a vertical shift is resultedin the whole of my curve.
> Is not it strong(wonderfull?)?
> 

I don't completely understand this comment.  You can control the position of the 
zero value of the PMF using g_wham -zprof0.  Since DeltaG is relative, you can 
choose a location for the zero point however you like.  I generally set the zero 
point somewhere out where the PMF curve has leveled off (i.e., no interaction 
between the pulled group and the reference).  If your curve is shifting 
dramatically when adding windows, you probably aren't anywhere close to 
achieving a stable result and you will need substantially more simulation time 
in each window.

-Justin

-- 
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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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