I am using md-vv as an integrator but if I use m , I don't see this drift (movement) in my system. This is also another problem that I could not figure out.
On Mon, Jun 15, 2015 at 6:04 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > Hi Mark, > > What do you mean by saying "thing"? Is phase changing? > > I visualized in VMD but could not manage to really captured the difference > before 7.5 ns and after 7.5 ns. > Also because during the simulation all bulk is moving in the box but > distances between pullgroups stays constant so it is not easy to capture > what is going on there. > > On Mon, Jun 15, 2015 at 5:58 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> 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. >> > > -- 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.