[gmx-users] Regarding umbrella samplling

[Dr. Vitaly Chaban]

Yes, it means what you say.

I would decrease the number of bins.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Oct 13, 2014 at 12:47 PM, 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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