Re: [AMBER] Problem related to the RMSD

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 3 Nov 2012 11:43:20 -0400

This is almost certainly an artifact caused by something happening that you didn't expect.

You should look carefully at the exact way that you computed the RMSD. For instance, did you align all of the structures? Did you select only those residues you meant to?

Visualizing your full trajectory will probably help you determine what happened. The RMSD is a simple metric, so anything that makes the RMSD jump that significantly should be clearly visible when you actually look at your system.

In order for us to help more than this, we will have to know how you calculated the RMSD (i.e., what program? What exact command did you use? Etc.)

Good luck,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 3, 2012, at 10:25 AM, Sindrila Dutta banik <sindrila.duttabanik.yahoo.com> wrote:
> Dear all,
>  
> I generated trajectory for 3 ns. For first 800 ps, I do 50 ps at a time. After this I generate trajectory for 200 ps at a time. As I am going to analyze the result it shows a unnatural result. I computed the RMSD and the result is natural upto 800 ps. After 800 ps, as time increase by 191.3 ps suddenly the RMSD increases too much. And after 200 ps again it comes down. The plot is shown in the attached file. Please have a look and let me know what it the problem. 
>  
> With best regards
> Sindrila
> <Time vs RMSD plot.doc>
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Received on Sat Nov 03 2012 - 09:00:02 PDT