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
