[gmx-users] pmf_calculation

[Justin A. Lemkul]

shahid nayeem wrote:
> Please the histogram generated. It does not show any window overlap.

You have some regions where the overlap is good, some where it is weak, and some 
where it is nonexistent.  You either need more sampling or more windows to 
capture the entire reaction coordinate.  This is discussed in the tutorial.

-Justin

> Shahid nayeem
> 
> On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     shahid nayeem wrote:
> 
>         Dear Justin
>         I did pmf calculation for my protein-protein complex using your
>         tutorial.Off course changing the pull_direction suitable for my
>         protein but more or less following the same strategy. I am using
>         gromacs_4.5.4 and g_wham utility. The profile.xvg file which I
>         get is attached and it shows two dips in PE curve. Please see it
>         and tell me why I am getting these dips.
> 
> 
>     You have insufficient sampling in at least these two regions.  Your
>     histograms should confirm this.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================