[gmx-users] Regarding umbrella samplling

[Johnny Lu]

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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