On Mon, May 6, 2013 at 3:48 AM, Kong xq <xqkong...@gmail.com> wrote: > Hi Mark, > > > Thanks for your great help. I am sorry for the negligence to state the > variation value correctly( it should be 0.011 rather than 0.11). Does this > somewhat small value indicate the generalized equilibrium achieved?
It might be consistent with it, but it is never diagnostic of it. FWIW, I have never seen an REMD study that attempted to address whether generalized equilibrium was achieved. I will > search the papers you suggested. I am wondering whether the histogram is > the gold standard for effectively constructing REMD flow. Moreover, how to > do the potential energy overlap analysis in Gromacs, from the edr file for > each replica ？Does any tool avalible in Gromacs to do this job ? > g_energy to get the data for each replica, then your favorite analysis package to form histograms, and graphing program to overlay the plots. The histograms can be done with g_analyze. Mark -- 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
