[gmx-users] pmf_calculation

[Justin A. Lemkul]

shahid nayeem wrote:
> I used following command
> g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
> Both profile.xvg and hist.xvg are created with this command using same 
> pullf.xvg and .tpr files.

An identical command with identical input files producing totally different 
output?  Sorry, but I find that hard to believe.  Check your work and make sure 
you're using the input you think you are.  I suspect something's amiss and 
you're not seeing it.

-Justin

> shahid Nayeem
> 
> On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <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 <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

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