Hi, Your trajectory went from one thing to a completely different thing, so what did your visual inspection of the trajectory tell you?
Mark On Mon, 15 Jun 2015 17:54 gozde ergin <gozdeeer...@gmail.com> wrote: > Hi all, > > My system has 560 water molecules covered by 50 organic molecules. I run > the simulation for 20 ns and here is my potential energy figure. > > http://imgur.com/l9mJesD,ggDDZtb#0 (first pic) > > > I just could not understand what is going on after 7.5 ns? > > Also I am doing this simulation to calculate the PMF. On the links there > are two PMF curves for the same system for 4ns and 20ns. They are pretty > different! (4 ns seems more realistic) > > http://imgur.com/l9mJesD,ggDDZtb#0 (second pic). > > What could be the reason to get two very different PMF curve for the same > system? > > bests > -- > 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.