[gmx-users] g_wham error

[Justin A. Lemkul]

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>> 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>> 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> | (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
> 
> 
> 
> 
> -- 
> 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

========================================