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

From: Jason Swails <>
Date: Thu, 4 Jun 2015 12:17:44 -0400

On Thu, Jun 4, 2015 at 9:59 AM, jacob wick <> 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
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).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jun 04 2015 - 09:30:06 PDT
Custom Search