Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time

From: Jason Swails <>
Date: Thu, 4 Jun 2015 09:51:00 -0400

On Thu, Jun 4, 2015 at 9:38 AM, jacob wick <> wrote:

> Hi everybody,
> I have simulated a DNA molecule for about 40ns and after analyzing the
> trajectory what I got to know is that the two strands of DNA are going away
> ( I would say fluctuation of the double helix was observed) for a very
> short interval of time and then they are again showing the usual double
> helix structure. The backbone RMSD (after re-imaging the trajectory) with
> the simulation length was observed as:

​Still sounds like an imaging artifact. The fact that it "jumps" between
large and small RMSDs is a tell-tale sign of imaging artifacts.

How did you do the imaging? If you didn't use the "autoimage" command, I
suggest using that instead.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 04 2015 - 07:00:04 PDT
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