Hi Jason,
Yes, I am working on 29 base pairs DNA system.
Now everything is looking fine after using autoimage command.
Thanks for the help and advice.
Jac
On Thu, Jun 4, 2015 at 9:47 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jun 4, 2015 at 9:59 AM, jacob wick <jacobwick.la.gmail.com> wrote:
>
> > Thanks for your reply!
> >
> > For reimaging:
> > trajin prod1.mdcrd
> > trajout prod1_reimaged.mdcrd
> > center :1-58
> > image familiar
> >
>
> Do you have two 29-residue DNA strands? If so, centering on both strands
> and reimaging around that will not fix the cross-box "jumps" that one of
> the strands does during the simulation -- in fact, it will ensure that
> those jumps *won't* be removed.
>
> Instead, you would want to center on a *single* strand, and image the other
> strand to that one. Imaging is a tricky thing, and there are an infinite
> number of ways to image your system (since the system is infinitely
> periodic). The 'autoimage' command *typically* does what most people want
> it to, so you should always try that one first. Your command above
> becomes:
>
> trajin prod1.mdcrd
> autoimage
> trajout prod1_reimaged.mdcrd
>
> (Also, I would suggest switching to NetCDF files instead of mdcrd using
> "ioutfm=1" in the sander/pmemd input file and using the ".nc" file suffix
> or "netcdf" trajout keyword -- NetCDF files are higher precision, many
> times faster to both read and write, and more resistant to errors like
> coordinate overflowing).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 05 2015 - 01:30:08 PDT
