On Thu, Jun 4, 2015 at 7:59 AM, jacob wick <jacobwick.la.gmail.com> wrote:
>
> For reimaging:
> trajin prod1.mdcrd
> trajout prod1_reimaged.mdcrd
> center :1-58
> image familiar
>
As Jason suggested, try replacing your center/image commands with
'autoimage' - see if that eliminates the "jumps" you were seeing.
-Dan
>
>
> 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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> >
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 04 2015 - 08:30:02 PDT
