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
<<attachment: rmsd_calpha.png>>
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