[gmx-users] g_wham error

rajat desikan rajatdesikan at gmail.com
Sun Nov 20 22:24:56 CET 2011


Justin,
Should i turn off charges on the methane molecules? I have left them on.

On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul <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>> 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**>__>> 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>>> 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> |
>>        (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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>> >>
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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
>>
>>        ------------------------------**__----------------------------**
>> --__------------
>>
>>
>>
>>    --     ==============================**__==========
>>
>>    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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>> --
>> Rajat Desikan (Ph.D Scholar)
>> 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<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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