[gmx-users] g_wham error
Justin A. Lemkul
jalemkul at vt.edu
Sun Nov 20 22:35:47 CET 2011
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>> 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>>> 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 <mailto:rajatdesikan at gmail.com>
> <mailto:rajatdesikan at gmail.com <mailto:rajatdesikan at gmail.com>__>
> <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>
> <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
> 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
>
> --
> ==============================______==========
>
>
>
> 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
>
> http://www.bevanlab.biochem.______vt.edu/Pages/Personal/justin
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> -- Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>
>
>
>
> -- Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>
>
> ------------------------------____----------------------------__--__------------
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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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> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>
> ------------------------------__------------------------------__------------
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> ------------------------------__------------------------------__------------
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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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> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> 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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