[gmx-users] PMF curve

[Justin A. Lemkul]

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.

> 
> 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.

>     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.

>     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.

-Justin

-- 
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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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