[gmx-users] PMF curve

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Mon May 30 17:08:29 CEST 2011

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
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?

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

Sorry,my english is not very good
Thanks in advance for your reply

On Mon, May 30, 2011 at 7:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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