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.lu...@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 <sathishk...@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-requ...@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-requ...@gromacs.org. > -- regards M.SathishKumar -- 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.