[gmx-users] RMSD sudden jump

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 13 10:09:15 CET 2012

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.



On Tue, Mar 13, 2012 at 6:49 AM, Davide Mercadante
<dmer018 at 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
> --
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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

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