Re: [AMBER] Regarding molecule's breaking during simulation.

From: Jason Swails <>
Date: Mon, 02 Jun 2014 08:12:38 -0400

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:



Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 02 2014 - 05:30:04 PDT
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