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

[Anirban Ghosh]

Thanks a lot for the reply.
Actually I am running a protein in lipid bilayer. Now I want to
calculate the thickness of the bilayer at the end of the simulation.
So for that I want the last structure (.gro) file. So I am trying to
dump the last structure using trjconv (with -pbc option). So to do
this which .tpr file should I supply to trjconv, the first one or the
last one?

Thanks again.

Anirban

On 12/4/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
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