[AMBER] Regarding molecule's breaking during simulation.

From: richa anand <richaaanand.gmail.com>
Date: Mon, 2 Jun 2014 17:22:09 +0530

Hi Amber Users,

I performed the MD simulation of siRNA-Protein complex for 100 ns, but
after 13ns siRNA molecule get detached from the cavity of protein and after
18ns run siRNA reattached in the cavity of protein. And this has occurred
around 80ns also. Due to this detachment, RMSD against C-Alpha atoms are
reaching to 25-45 Å. I am sending the snapshot of the trajectory movie.
Please help me to understand the reason behind such high RMSD fluctuation.
I have used force-fields :rna.ff02 and ff12SB, and in both cases I
encountered the same problem of such high RMSD fluctuation.

Any suggestion and help is highly appreciated. Thanks in advance.




Thanking You,
Richa
IIIT Allahabad
India.


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Received on Mon Jun 02 2014 - 05:00:04 PDT
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