[gmx-users] PMF curve
Justin A. Lemkul
jalemkul at vt.edu
Mon May 30 16:44:19 CEST 2011
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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