Sorry I realized I attached the .xvg.<br><br>Here is a png for a easier visualization. Sorry for the inconvenience.<br><br>Thanks,<br>Davide<br><br><div class="gmail_quote">2012/3/14 Davide Mercadante <span dir="ltr"><<a href="mailto:dmer018@aucklanduni.ac.nz">dmer018@aucklanduni.ac.nz</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Tsjerk,<br><br>thanks very much for your prompt reply. <br>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). <br>
<br>However, the switch seems unlikely as the protein seems to lose part of its fold.?! <br>Could that be an artifact of the forcefield or something similar? <br><br>Should I repeat the MD using a different ff? Could this help?<br>
<br>Thanks in advance for your reply.<br><br>Cheers,<br>Davide<div class="HOEnZb"><div class="h5"><br><br><div class="gmail_quote">
2012/3/13 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Davide,<br>
<br>
If you've checked the trajectory, and you've assured that there are no<br>
atoms wrapping over the periodic boundaries, and you've noticed a<br>
sudden change in conformation, then probably that's what it is: a<br>
sudden change in conformation. That does agree with the plot. After a<br>
rather stationary phase, close to the reference structure, the<br>
molecule undergoes a transition to another state. To see if it<br>
converges in that state in the time of your simulations, get the<br>
average structure from the last 5 ns of the simulation and run the<br>
RMSD against that.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div><br>
On Tue, Mar 13, 2012 at 6:49 AM, Davide Mercadante<br>
<<a href="mailto:dmer018@aucklanduni.ac.nz" target="_blank">dmer018@aucklanduni.ac.nz</a>> wrote:<br>
> Dear gromacs users,<br>
><br>
> I have performed ~30ns MD on a protein in TIP4P water using the OPLS<br>
> forcefield.<br>
> I have concatenated the trajectories for each step using trjcat and removed<br>
> pbc effects using pbc nojump.<br>
><br>
> All the particles of the system now don't jump anymore and the molecule<br>
> doesn't appear as broken.<br>
><br>
> However, at some point from the beginning of the simulation the RMSD jumps<br>
> up as in the graphs attached.<br>
> Visualizing the trajectories from that point the protein just suddenly<br>
> change conformation and its motions become faster (as testified by the<br>
> RMSD).<br>
><br>
> Can you please let me understand why this happens? If I have screwed<br>
> something up with the calculation or if something due to the pbc effects not<br>
> removed properly?<br>
> The same thing is also happening on a different simulations involving a<br>
> 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>
><br>
</div></div>> --<br>
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<span><font color="#888888"><br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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</font></span></blockquote></div><br><br clear="all"><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>
</div></div></blockquote></div><br><br clear="all"><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>