[gmx-users] PMF curve

[mohsen ramezanpour]

Yes,you are right
I need to do more sampling.But the second attached file was just  to
transfer my mean :)
My final PMF curve is the first attached file.

Sorry for asking more questions..

Regarding my notes about windowses in last email and looking at FIRST
attached file:
Which one is my starting point?
0.18 (with negative value ) OR 0.03 (with about zero value) OR the average
in that region?

Because there is a difference about  0.5 kcal/mol .
Thanks in advance




On Mon, May 30, 2011 at 7:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 unconverged.
>
>
> -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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