[gmx-users] Regarding umbrella samplling

[Sathish Kumar]

I am not able to find wheather the windows are overlaped or not. Please
help me in this.

Thanks.

On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar <sathishk238 at gmail.com>
wrote:

> 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
>



-- 
regards
M.SathishKumar