[gmx-users] RMSD sudden jump

Davide Mercadante dmer018 at aucklanduni.ac.nz
Tue Mar 13 06:49:47 CET 2012

Dear gromacs users,

I have performed ~30ns MD on a protein in TIP4P water using the OPLS
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

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 Mercadante - PhD student -
School of Chemical Sciences
The University of Auckland
1142 Auckland, New Zealand
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