[gmx-users] g_wham error
Justin A. Lemkul
jalemkul at vt.edu
Sun Nov 20 22:58:07 CET 2011
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>> 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>>> 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>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <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
> <mailto:rajatdesikan at gmail.com>
> <mailto:rajatdesikan at gmail.com
> <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>
> <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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> ==============================________==========
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> ------------------------------______--------------------------__--__--__------------
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> -- ==============================______==========
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> ------------------------------____----------------------------__--__------------
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> -- ==============================____==========
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> Justin A. Lemkul
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> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
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> ==============================__==========
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> Justin A. Lemkul
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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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