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-requ...@gromacs.org.