Anirban Ghosh wrote:
Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure?

That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state?

like when I an using trjconv to dump my last frame (with "-pbc nojump"), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file?


I don't understand what you mean. "What has happened" is an entire trajectory, not a snapshot.

-Justin

Thanks a lot again.

Anirban
On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:



    Anirban Ghosh wrote:

        Hi ALL,

        Its a very basic question but still...
        When we calculate RMSD (or any other parameter) using the g_rms
        command, we need to supply the .tpr file with -s option. Now
        suppose if I have a total 20 ns simulation with 4 breaks (i.e 5
        ns in each run), then there will be 4 .tpr files. So at the end
        of 20 ns if I wish to calculate RMSD, then which .tpr file
        should I suppy to g_rms, the first one or the last one? We I run
        g_rms with the two .tpr files, I get different results. So which
        one should be used? Any suggestion is welcome.


    Use the one that contains the structure you wish to serve as your
    reference.

    -Justin


        Thanks,

        Anirban


-- ========================================

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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