[gmx-users] RMSD sudden jump

[Davide Mercadante]

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 <dmer018 at aucklanduni.ac.nz>

> 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 <tsjerkw at gmail.com>
>
>> 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
>> <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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>
>
>
> --
> 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
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