[gmx-users] Regarding umbrella samplling

[Sathish Kumar]

Hai
      Yes, I have ploted the histogram, all windows are merged..please
check this histo.jpg file attached to the below link.

https://www.dropbox.com/s/ndl0w250dnawmib/histogram.jpg?dl=0



On Mon, Oct 13, 2014 at 3:47 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi. Does that mean the umbrella don't overlap enough at those z ?
> Can you make an overlay plot of the histograms of each umbrella?
>
> On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar <sathishk238 at gmail.com>
> wrote:
>
> > Dear gromacs usres,
> >
> >  I have run the umbrella sampling with the help of tutorial of justin. In
> > my system rna is binding with gold nanoparticle. To find out the binding
> > energy, i run the umbrella sampling using the space 0.1 nm and i got
> total
> > 79 configurations, each configuration was run for 5 ns. Using g_wham, i
> got
> > the profile.xvg, in that profile.xvg,  all PMF values are zero. while
> > running g_wham i am getting warings like below.
> >
> > WARNING, no data point in bin 163 (z=8.27767) !
> > You may not get a reasonable profile. Check your histograms!
> >
> > WARNING, no data point in bin 164 (z=8.31563) !
> > You may not get a reasonable profile. Check your histograms!
> >
> > WARNING, no data point in bin 165 (z=8.35358) !
> > You may not get a reasonable profile. Check your histograms!
> > Warning, poor sampling bin 194 (z=9.45432). Check your histograms!
> > Initialized rapid wham stuff (contrib tolerance 1.31579e-08)
> > Evaluating only 2619 of 15200 expressions.
> >
> >            1) Maximum change 3.178184e+02
> >          100) Maximum change 1.611126e+00
> >          200) Maximum change 3.303540e+00
> >          300) Maximum change 1.239682e+00
> >          400) Maximum change 1.383353e+00
> >          500) Maximum change 1.116406e+00
> >          600) Maximum change 1.241516e+00
> >          700) Maximum change 1.028108e+00
> >          800) Maximum change 1.698508e+00
> >          900) Maximum change 1.331078e+00
> > Switched to exact iteration in iteration 983
> > Converged in 984 iterations. Final maximum change 0
> >
> > Please help me in this regard.
> >
> > Thanks
> > sathish
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-- 
regards
M.SathishKumar