Sorry I realized I attached the .xvg. Here is a png for a easier visualization. Sorry for the inconvenience.
Thanks, Davide 2012/3/14 Davide Mercadante <dmer...@aucklanduni.ac.nz> > Hi Tsjerk, > > thanks very much for your prompt reply. > I checked the last 5ns rmsd against an average structure calculated in the > same time range and effectively the system seems to be converging (I > attached the graph). > > However, the switch seems unlikely as the protein seems to lose part of > its fold.?! > Could that be an artifact of the forcefield or something similar? > > Should I repeat the MD using a different ff? Could this help? > > Thanks in advance for your reply. > > Cheers, > Davide > > > 2012/3/13 Tsjerk Wassenaar <tsje...@gmail.com> > >> 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 >> > > > > -- > Davide Mercadante - PhD student - > School of Chemical Sciences > The University of Auckland > 1142 Auckland, New Zealand > > > > -- Davide Mercadante - PhD student - School of Chemical Sciences The University of Auckland 1142 Auckland, New Zealand
<<attachment: last5ns_RMSD.png>>
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