Hi Davide, If you've checked the trajectory, and you've assured that there are no atoms wrapping over the periodic boundaries, and you've noticed a sudden change in conformation, then probably that's what it is: a sudden change in conformation. That does agree with the plot. After a rather stationary phase, close to the reference structure, the molecule undergoes a transition to another state. To see if it converges in that state in the time of your simulations, get the average structure from the last 5 ns of the simulation and run the RMSD against that.
Cheers, Tsjerk On Tue, Mar 13, 2012 at 6:49 AM, Davide Mercadante <dmer...@aucklanduni.ac.nz> wrote: > Dear gromacs users, > > I have performed ~30ns MD on a protein in TIP4P water using the OPLS > forcefield. > I have concatenated the trajectories for each step using trjcat and removed > pbc effects using pbc nojump. > > All the particles of the system now don't jump anymore and the molecule > doesn't appear as broken. > > However, at some point from the beginning of the simulation the RMSD jumps > up as in the graphs attached. > Visualizing the trajectories from that point the protein just suddenly > change conformation and its motions become faster (as testified by the > RMSD). > > Can you please let me understand why this happens? If I have screwed > something up with the calculation or if something due to the pbc effects not > removed properly? > The same thing is also happening on a different simulations involving a > mutant of this protein... > > Any help will be very much highly appreciated! > > Thank you! > Davide > > -- > Davide Mercadante - PhD student - > School of Chemical Sciences > The University of Auckland > 1142 Auckland, New Zealand > > > > > -- > 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
