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

[Anirban Ghosh]

Thanks a lot for the reply.
But I am getting different results with the two .tpr files (first and last)
using the following commands:

trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 10000 -pbc nojump
trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 10000 -pbc nojump

So which .tpr file should I use?

Thanks,

Anirban

On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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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