Hi, Thanks. And the file Rg.xvg looks sound?
Kind regards, Erik > On 23 Jan 2017, at 11:33, faride badalkhani <farideh.kham...@gmail.com> wrote: > > Hi, > > Thanks for the answer. I used the autocorrelation function of the squared > radius of gyration cross-correlation of time course of Rg with itself with > the following command > gmx analyze -f Rg.xvg -ac > > and the autocorrelation is exactly zero. > > it is worth mentioning that I have performed the same PMF calculations on a > polymer-drug system and I did not have any problem in that case. The only > difference of that system with this one was in the terminal groups of > polymer. The first polymer has protonated surface groups (NH3+) but the > second one is neutral (acetylene). > > Best, > F. > > On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund <erik.markl...@kemi.uu.se> > wrote: > >> Dear Farideh, >> >> Can you please inform us about how you calculated the ac? Hard to help >> otherwise. Also, is it exactly zero or just very small numbers? >> >> Kind regards, >> Erik >> >>> On 23 Jan 2017, at 10:50, faride badalkhani <farideh.kham...@gmail.com> >> wrote: >>> >>> Dear GROMACS users, >>> >>> I am performing umbrella sampling on a polymer-ligand system and I >> generate >>> configurations successfully but the problem is that when I plot the >>> autocorrelation function of Rg for each window it is zero for the whole >>> time of simulation. I changed the run time for each window but nothing >>> changed. Moreover, the initial polymer-ligand structure is equilibrated >>> well. >>> Any comment or suggestion will be greatly appreciated. >>> >>> Best, >>> Farideh >>> -- >>> 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. >> > -- > 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.