[gmx-users] pmf_calculation

[Justin A. Lemkul]

shahid nayeem wrote:
> Dear Justin
> I did some more sampling and sending you profile.xvg, histo.xvg. and 
> hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell 
> my the difference in profile.xvg and hist.xvg. Both should be same but I 
> get different curves here.
> 

I can't tell you the difference because you haven't shown how they were 
generated.  My blind guess is that hist.xvg (a very confusing name for a PMF 
profile) was generated from data that have poor sampling in two regions.  The 
contents of profile.xvg look normal.  I don't know which of these curves 
corresponds to histo.xvg, because the histograms therein look fine.

Please make sure to give full descriptions of these files.  You've quote a 
message that is over a month old.  I've replied to hundreds of messages since 
then and I do not remember the full context of our discussion.

-Justin

> 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

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