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

Anirban Ghosh reach.anirban.ghosh at gmail.com
Fri Dec 3 18:04:31 CET 2010


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?
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?

Thanks a lot again.

Anirban

On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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