I use ptraj to compute the RMSD. The corresponding script file is as follows:
trajin MD16a.mdcrd
trajin MD16b.mdcrd
trajin MD17.mdcrd
trajin MD18.mdcrd
trajin MD19.mdcrd
trajin MD20.mdcrd
trajin MD21.mdcrd
trajin MD22.mdcrd
trajin MD23.mdcrd
trajin MD24.mdcrd
trajin MD25.mdcrd
trajin MD26.mdcrd
trajin MD27.mdcrd
trajin MD28.mdcrd
trajin MD29.mdcrd
trajin MD30.mdcrd
trajin MD31.mdcrd
trajin MD32.mdcrd
trajin MD33.mdcrd
trajin MD34.mdcrd
rms first out Backbone-A.dat :1-396.CA,N,C time 0.1
rms first out Backbone-B.dat :398-793.CA,N,C time 0.1
rms first out All-A.dat :1-396 time 0.1
rms first out All-B.dat :398-793 time 0.1
rms first out Heavyatom-A.dat :1-396&(!.H=) time 0.1
rms first out Heavyatom-B.dat :398-793&(!.H=) time 0.1
rms first out Protein_Substrate.dat :1-794 time 0.1
rms first out Backbone.dat :1-396,398-793.CA,N,C time 0.1
rms first out All.dat :1-396,398-793 time 0.1
rms first out Heavyatom.dat :1-396,398-793&(!.H=) time 0.1
I try to load the trajectory file in vmd, but as I am going to load it stop working might be due to large file size.
I also generated pdb file from each restrt file and overlay all of them using vmd. And the RMSD is less than 2 as computed by vmd.
Now where is the problem, I my trajectory or the process I use to compute the trajectory. How can I solve this problem. Please help me
Sindrila
From: Jason Swails <jason.swails.gmail.com>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER MailingList <amber.ambermd.org>
Sent: Saturday, 3 November 2012 9:13 PM
Subject: Re: [AMBER] Problem related to the RMSD
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 - 23:00:02 PDT
