[gmx-users] pmf_calculation

[shahid nayeem]

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.
shahid Nayeem

On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul <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>> 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
>>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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