[gmx-users] PMF curve

[mohsen ramezanpour]

On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> There is not any answer?
>>
>>
> Please have a bit of patience.  I'm not your personal answer service.  You
> just happened to catch me at a good time this morning and I was able to
> respond quickly.  I have my own work to do, you know.


Thanks for your reply
No Dr.Justin,I didn't mean this by my question.It was your favour replying
to my questions.
I  just thought my question is not logical OR it is answer is not difficult
And I must review articles in this field.just this.

>
>
>
>> On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour <
>> ramezanpour.mohsen at gmail.com <mailto:ramezanpour.mohsen at gmail.com>>
>> wrote:
>>
>>    Yes,you are right
>>    I need to do more sampling.But the second attached file was just  to
>>    transfer my mean :)
>>
>
> Always provide complete information.  I can't get in your head to know
> everything you're thinking.  If you want free help, make it easy to help
> you. Hack job files wind up causing confusion and delaying an answer rather
> than providing you with one.


Yes,You are right

>
>
>     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?
>>
>>
> I have no idea.  Watch your trajectories and see what your ligand is doing
> at these points.  Presumably you have a window in which the ligand is bound
> in the protein's active/receptor site, and perhaps after some simulation the
> position moves to arrive at its energy minimum.  In general, from a PMF
> curve, the highest point (as long as it's stable) minus the lowest point is
> your DeltaG.


aha!

>
>
>     Because there is a difference about  0.5 kcal/mol .
>>
>
> So there are some energetic differences in these windows.  Watch the
> trajectories to figure out why.
>


> Sure
>
> -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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