Re: [AMBER] High RMSD values due to use of iwrap

From: Jason Swails <>
Date: Fri, 8 Jan 2016 06:44:11 -0500

On Fri, Jan 8, 2016 at 6:09 AM, richa anand <> wrote:

> Hi Amber Users,
> I performed the MD simulation of 50 ns for RNA-Protein complex with iwrap =
> 0. But after 45 ns simulation got stuck. The error was: it could not
> identify the co-ordinates. To run whole simulation then I used iwrap = 1.
> It run for 50 ns, but when I measured RMSD values for C-alpha pf protein it
> went to 14-20 A.
> I am confused that when I use iwrap why I get high values of RMSD, while
> the same input file to calculate RMSD gives low values of RMSD without
> using iwrap (i.e. iwrap = 0). But using iwrap = 0 simulation get stuck
> after 45 ns.

​What is probably happening is that the protein and RNA chains are being
imaged separately (that is, the trajectory will appear to show the RNA or
protein "jump" to the other side of the box while the other one stays
put). This is an artifact, since each image of the protein is still
interacting with an image of the RNA, and vice versa. What you need to do
is make sure you create a representation consistent with the interaction
you hope to study (i.e., the interacting pair).

> Please suggest me how to get right values of RMSD. I used 'image' command
> ​​
> during RMSD calculation.

​Chances are if you used the "image" command, it was not constructed
correctly to bring the chains back together. You typically need a rather
complex combination of "center" and "image" to ensure that you image the
two biomolecule chains independently (if you always image them together,
they will not "re-combine"). Of course, since you didn't actually tell us
the exact commands you ran, all we can do is guess.

Instead of using the "image" command, use "autoimage", which simplifies the
imaging process. You can replace all of the "center" and "image" commands
in your cpptraj script with "autoimage".


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 08 2016 - 04:00:05 PST
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