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
Received on Thu Jun 04 2015 - 09:30:06 PDT
