Re: [gmx-users] RMSD sudden jump
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 > 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 > >> 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 >> 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 listgmx-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 listgmx-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 <>-- gmx-users mailing listgmx-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
Re: [gmx-users] RMSD sudden jump
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 > 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 > 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 listgmx-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 listgmx-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 rmsd_calpha_last5ns.xvg Description: Binary data -- gmx-users mailing listgmx-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
Re: [gmx-users] RMSD sudden jump
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 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 listgmx-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
[gmx-users] RMSD sudden jump
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 listgmx-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
