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

[Mark Abraham]

On 4/12/2010 4:33 PM, Anirban Ghosh wrote:
> 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?

Since you're not using the coordinates in the .tpr file to extract the 
last frame and map its coordinates onto the .tpr's atom names, it can't 
matter what they are.

Mark

> 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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