Dear gromacs users,<br><br>I have performed ~30ns MD on a protein in TIP4P water using the OPLS forcefield. <br>I have concatenated the trajectories for each step using trjcat and removed pbc effects using pbc nojump.<br><br>
All the particles of the system now don't jump anymore and the molecule doesn't appear as broken. <br><br>However, at some point from the beginning of the simulation the RMSD jumps up as in the graphs attached. <br>
Visualizing the trajectories from that point the protein just suddenly change conformation and its motions become faster (as testified by the RMSD).<br><br>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? <br>
The same thing is also happening on a different simulations involving a mutant of this protein...<br><br>Any help will be very much highly appreciated!<br><br>Thank you!<br>Davide<br><br>-- <br>Davide Mercadante - PhD student -<br>
School of Chemical Sciences<br>The University of Auckland<br>1142 Auckland, New Zealand<br><br><br><br>