Dear Justin, I am very thankful to you for your reply, you are correct, I have plotted the histo.xvg file in wrong manner. After plotting histograms in correct manner I have realized that my sampling is very poor as histograms and there overlapping is restricted to some regions only, no histograms in some areas along reaction co-ordinate. I am not sure whether this lack of sampling is due to inappropriate selection of pulled configurations or inappropriate pull geometry. However I will try as per your suggestion and get back to you.
Thank you, Regards, Ramesh. On Mon, Nov 26, 2012 at 7:39 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/26/12 1:03 AM, ramesh cheerla wrote: > >> Dear Gromacs users, >> >> >> I am calculating PMF for the ion permeation through a tunnel, using >> umbrella sampling. In my system I have some binding sites with ions, I >> have >> removed some ions from binding sites before pulling and In pulling >> simulations have pullaed pulled the adjacent ions to the vacant binding >> site (tunnel is aligned along Y- axis). >> for this I have used the following options in .mdp file. >> ; Pull code >> pull = umbrella >> pull_geometry = distance >> pull_dim = N Y N >> pull_start = yes >> pull_ngroups = 1 >> pull_group0 = REFA >> pull_rate1 = 0.01 >> pull_k1 = 3000 ; kJ mol^-1 nm^-2 >> >> Here pull_group0 = REFA is the ion at another binding site and >> pull_group1 = ATBP is the atom that I am pulling to the vacant site. >> In next step I have performed umbrella sampling simulations to the >> selected >> configurations using the following options : >> ; Pull code >> pull = umbrella >> pull_geometry = distance ; simple distance increase >> pull_dim = N Y N >> pull_start = yes ; define initial COM distance > 0 >> pull_ngroups = 1 >> pull_group0 = REFA >> pull_group1 = ATBP >> pull_init1 = 0 >> pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns >> pull_k1 = 3000 ; kJ mol^-1 nm^-2 >> pull_nstxout = 100 >> pull_nstfout = 100 >> After that I have constructed PMF profile using Gromacs tool "g_wham", >> while using g_wham I am getting the following warnings, >> "WARNING, no data point in bin 34 (z=0.889382) ! >> You may not get a reasonable profile. Check your histograms!" >> I have checked my histograms instead of one histogram for each >> configuration with perfect overlapping, I am getting only one histogram. >> > > You're probably just plotting the file wrong. > > xmgrace -nxy histo.xvg > > > Here I am sending the link that containing PMF profile and histogram that >> have obtained. >> http://researchweb.iiit.ac.in/**~bipin.singh/pmf.jpg<http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg> >> http://researchweb.iiit.ac.in/**~bipin.singh/hist.jpg<http://researchweb.iiit.ac.in/~bipin.singh/hist.jpg> >> >> > The PMF suggests massive undersampling (or complete lack of sampling) in > several areas. > > > the weired thing that I have observed in my pulling simulations is that I >> have expected motion of ion in positive Y-direction for my pull parameters >> but it is moving in negative Y- direction. >> Can anybody please suggest me a solution for this, Am I following >> correct >> protocol to get PMF of my system, is there any better method that suits >> for >> my system. >> >> > If you are trying to see a complete translocation of an ion through a > channel, the "distance" geometry is inappropriate, as it does not deal > correctly with the change of sign for the vector between the reference and > pulled group, IIRC. Try "position" geometry and associated settings. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists