[gmx-users] g_wham error
Justin A. Lemkul
jalemkul at vt.edu
Sun Nov 20 23:08:42 CET 2011
rajat desikan wrote:
> Sorry, sorry...I have used Opls AA. The methane was going back and forth
> in the pulling during which I generated the configurations.
>
Assuming you used a harmonic potential, that is to be expected. As long as you
have set up reasonable spacing for your sampling windows from the snapshots
along that trajectory, that should not be an issue. I also see no reason for
uneven spacing in a system as simple as this one, though that's not a problem,
per se, just not necessary.
-Justin
> On Mon, Nov 21, 2011 at 3:28 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> rajat desikan wrote:
>
> Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on
> the hydrogens...I am using Gromos 96 53a6 force field. I am
> getting a couple
>
>
> This is fundamentally incorrect. 53A6 is a united-atom force field,
> so each methane should be a single particle with 0 charge using the
> CH4 atom type.
>
>
> of doubts Justin. Since, I am pulling the methane away steadily,
> it should smoothly increase the distance right? But the second
> methane molecule is both increasing and decreasing it's
> position, sort of going back and forth.
>
>
> This sounds like SMD, not umbrella sampling. Or are you referring
> to the pulling during which you generated configurations for
> umbrella sampling?
>
>
> Also, one more thing. Originally, I had given the option for
> pull_dim as Y N N (x direction). But the second methane moved in
> all 3 directions.
>
>
> There is no reason to suppose that pulling in only one dimension
> will necessarily be correct. The dissociation of two simple
> molecules can occur in 3 dimensions.
>
>
> So I position restrained the second methane to the x axis
> (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on
> my simulations?
>
>
> It should be unnecessary to restrain either molecule.
>
> -Justin
>
> On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> rajat desikan wrote:
>
> Justin,
> Should i turn off charges on the methane molecules? I
> have left
> them on.
>
>
> What force field are you using? If you've got an all-atom
> model of
> methane, you should have partial charges.
>
> -Justin
>
> On Mon, Nov 21, 2011 at 12:32 AM, 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:
>
>
>
> rajat desikan wrote:
>
> My simulations are for 10 ns in each window. There
> is a
> lot of
> noise in my wham too. I am enclosing my wham for
> pullf (the
> earlier was pullx) and pmf. They are really
> looking strange.
> Stronger restraint means force constant? >From
> literature, I
> kept it at 3000.
>
>
> Those plots do look very strange. The PMF is almost a
> step
> function, which is certainly wrong. You may need
> either more
> simulation time or more frequent collection of data
> points,
> but at
> this stage I can only guess. Not much more I can
> offer, sorry.
>
> A stronger restraint would mean a stronger force constant,
> yes, but
> if you're using 3000 to restrain simple molecules like
> methane, I
> think there is no need to increase it.
>
> -Justin
>
> On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
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> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>> wrote:
>
>
>
> rajat desikan wrote:
>
> hi Justin
> I am not able to tell where the lack of overlap
> is. This
> is the
> first wham plot I am looking at. In your
> tutorial and
> literature, the wham plots are so clear.
> Can you
> please
> help me?
> Thanks.
>
>
> It looks like your first one or two windows
> were not
> restrained
> sufficiently at the desired distance. The
> error complains
> that bin
> 2 should have points at 0.366 nm, but it appears
> neither bin
> 1 nor
> bin 2 satisfy this requirement. Check carefully
> what
> you have set
> for reference distances and what distances were
> actually
> maintained
> during the sampling. You may need a stronger
> restraint or longer
> simulations. How long are the simulations? I see
> that you're
> starting the analysis on data after 2 ns, but
> how much
> does
> that leave?
>
> -Justin
>
> On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan
> <rajatdesikan at gmail.com
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> <mailto:rajatdesikan at gmail.com>__>__>__>__>> wrote:
>
> Oh lovely...thanks for the quick reply
> Justin :)...
>
>
> On Sat, Nov 19, 2011 at 10:57 PM, Justin
> A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
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> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>>> wrote:
>
>
>
> rajat desikan wrote:
>
> Hi
> I am a new gromacs user. I just
> completed Justin's
> umbrella
> sampling tutorial. I am doing a PMF
> calculation between 2
> methane molecules in water. The
> simulation has run
> fine till
> the g_wham step. My command is
>
> -- g_wham -it tpr-files.dat -if
> pullf-files.dat -o -hist
> -unit kCal -b 2000
>
> I get a warning:
> WARNING, no data point in bin 2
> (z=0.366256) !
> You may not get a reasonable
> profile.
> Check your
> histograms!
>
> and my histogram contains a
> single peak.
>
> I have pulled my other methane 1 nm
> away from
> the first
> methane. I have 15 sampling windows
> (0.05 nm apart
> till 5nm
> and then 1 nm apart)...can you
> please
> tell me
> how to
> correct
> this?
>
>
> With 15 windows, you should have 15
> histograms.
> Plot with:
>
> xmgrace -nxy histo.xvg
>
> It will show you where the lack of
> sampling is.
>
> -Justin
>
> --
> ==============================__________==========
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>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
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> -- Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
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> -- Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
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> ------------------------------________------------------------__--__--__--__------------
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>
>
> --
> ==============================________==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
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> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu>
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> ------------------------------______--------------------------__--__--__------------
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> -- ==============================______==========
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> Justin A. Lemkul
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>
> -- ==============================____==========
>
> Justin A. Lemkul
> Ph.D. Candidate
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> Blacksburg, VA
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> --
> ==============================__==========
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> Justin A. Lemkul
> Ph.D. Candidate
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> Indian Institute of Science, Bangalore
--
========================================
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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