Hi Melchor, Have you looked at the structures? The GROMOS people suggest using twin-range cut-off with reaction field correction, and the Vanderwaals cutoff you use seems a bit small, as 1.4 nm is commonly used with GROMOS. Maybe that makes a difference.
Cheers, Tsjerk On Tue, Jul 2, 2013 at 3:37 PM, Melchor S. <msm...@cid.csic.es> wrote: > I expected to see how the RMSD increases with time respect the closed > cristallographic structure and decreases with time respect to the open > crystal structure. > > I obtained it for OPLS, but with gromos I obtain a kind of mixture in that > you see that the structure behaves different between the open ad close > conformations at the beginning but then remain at thesame distance. You > don't see a clear differenciation between the closed and the open forms. > And > you have to see it. > > Forn calculate I used g_rmsd -d traj.trr -s Crystal_structure.gro -o > rmsd.xvg I do it over the backbone > > Also, I visualize it in VMD, loading the gro and the trr files, and the > the > crystal structures. Using the Trajectory analysis tool , I align the > strucutres and calculate the RMSD over the crystal structure. > > Something easy, not problematic in principle, but is giving me a lor of > problems with gromos, because I have repeated three times the simulation, > obtaining similar pictures as the one that you can see below. > > I want to know if there is some reason for this behaviour or not, Maybe you > need more time to equilibrate with gromos than with OPLS? > > For the initial setup of the simulation, I follow the same procedure in all > cases with the same settings, I even added manually the protonation states > of the terminal residues and also of the Histidines. > > OPLS > <http://gromacs.5086.x6.nabble.com/file/n5009497/OPLS2.png> > > Gromos > <http://gromacs.5086.x6.nabble.com/file/n5009497/Gromos.png> > > > cheers, > > Melchor S. > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Problem-calculating-RMSD-with-gromos-tp5009494p5009497.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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