[gmx-users] Regarding umbrella samplling

[Sathish Kumar]

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