[gmx-users] PMF curve

[mohsen ramezanpour]

Thank you for your reply

Actually my system is not the same as tutorial.
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))?

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?)?

On Mon, May 30, 2011 at 6:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ========================================
>
> 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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