[gmx-users] pmf_calculation
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 11 14:44:53 CEST 2011
shahid nayeem wrote:
> 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.
>
They cannot be simultaneous output. The file named "hist.xvg" contains a PMF
profile and has a date stamp of July 5 (in the .xvg header). The file
"profile.xvg" is also a PMF profile and a has a date of August 11. They were
not produced simultaneously. The file "histo.xvg" (with which you may be
confusing "hist.xvg") was produced alongside "profile.xvg" and contains the
umbrella sampling histograms, and was produced alongside "profile.xvg."
I think you've somehow lost track of which files are which. It seems that
"hist.xvg" contains the PMF profile from poor sampling, per our discussion a
month ago, and "profile.xvg" contains something newer, likely with better data.
-Justin
> On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>>
> <mailto: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>
> <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 <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
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