[gmx-users] Regarding umbrella samplling

[Sathish Kumar]

Hai
       I have decreased the number of bins=50 and i have not get the
previously mentioned warnings. Still, the profile.xvg is looking like below

 2.148184e+00    0.000000e+00
2.300988e+00    0.000000e+00
2.453792e+00    0.000000e+00
2.606596e+00    0.000000e+00
2.759400e+00    0.000000e+00
2.912204e+00    0.000000e+00
3.065009e+00    0.000000e+00
3.217813e+00    0.000000e+00
3.370617e+00    0.000000e+00
3.523421e+00    0.000000e+00
3.676225e+00    0.000000e+00
3.829029e+00    0.000000e+00
3.981833e+00    0.000000e+00
4.134637e+00    0.000000e+00
4.287441e+00    0.000000e+00
4.440246e+00    0.000000e+00
4.593050e+00    0.000000e+00
4.745854e+00    0.000000e+00
4.898658e+00    0.000000e+00
5.051462e+00    0.000000e+00
5.204266e+00    0.000000e+00
5.357070e+00    0.000000e+00
5.509874e+00    0.000000e+00
5.662678e+00    0.000000e+00
5.815483e+00    0.000000e+00
5.968287e+00    0.000000e+00

The value of PMF is coming zero kCa/mol.... If i neglect the 6 windows
before the last window then the pmf values are not zero. The obtained pmf
curve is attached to the below link.

https://www.dropbox.com/s/8tunpvfmnakupiu/pmf.jpg?dl=0

What may be reason could be? Can you please explain me. And please suggest
me how to solve this problem.

Thanks
sathish


On Mon, Oct 13, 2014 at 10:08 AM, Sathish Kumar <sathishk238 at gmail.com>
wrote:

> 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
>>> > --
>>> > Gromacs Users mailing list
>>> >
>>> > * Please search the archive at
>>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> > posting!
>>> >
>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> >
>>> > * For (un)subscribe requests visit
>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> > send a mail to gmx-users-request at gromacs.org.
>>> >
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
>>
>> --
>> regards
>> M.SathishKumar
>>
>
>
>
> --
> regards
> M.SathishKumar
>



-- 
regards
M.SathishKumar