On Mon, 2014-06-02 at 17:22 +0530, richa anand wrote:
> 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.
This might be an imaging artifact if you set iwrap=1 in your input file.
See if reimaging the trajectory "fixes" what you are seeing. You can
use the "autoimage" command in cpptraj to do this:
trajin your_trajectory.nc
autoimage
trajout new_trajectory.nc
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 02 2014 - 05:30:04 PDT
