[gmx-users] Which .tpr file to use for g_rms?

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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

========================================