[gmx-users] pmf_calculation
shahid nayeem
msnayeem at gmail.com
Thu Aug 11 14:30:16 CEST 2011
Both files hist.xvg and profile.xvg both are simultaneous output of this
command. I did not run it twice, once to get profile.xvg and then to get
hist.xvg as you uderstood.
On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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://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://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 | (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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