Thanks for your reply!
For reimaging:
trajin prod1.mdcrd
trajout prod1_reimaged.mdcrd
center :1-58
image familiar
For backbone RMSD:
trajin prod1_reimaged.mdcrd
rms first out finalbackbone.rms @P,O3',O5',C3',C4',C5' time 0.2
Regards,
Jac
On Thu, Jun 4, 2015 at 7:21 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jun 4, 2015 at 9:38 AM, jacob wick <jacobwick.la.gmail.com> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Jun 04 2015 - 07:00:05 PDT
