[gmx-users] Snapshot and co-ordinate query

[Ankita naithani]

Hi Justin,

Thank you so much for the clarification.


Kind regards,

Ankita


On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/5/13 3:03 PM, Ankita naithani wrote:
>
>> Hi,
>>
>> I have two questions.
>>
>> I have performed a simulation on my protein structure and after the
>> simulation, I used trjconv to obtain snapshots after every 10 ns with the
>> following command:
>>
>> trjconv -f md.xtc -s md.tpr -b 10000 -e 10001 -o md_10.pdb
>>
>>
> This command will produce one snapshot.  If you're looking to get multiple
> snapshots, it is easier to combine -skip -sep to write out multiple
> snapshots in one command.
>
>
>  and chose 0 (system) for the group.
>> However, when I see the same structure in PyMol as cartoon representation,
>> I see the protein structure and few of the residues scattered elsewhere of
>> a particular chain, say chain A. I am concerned whether my residues of
>> that
>> particular chain fragmented during simulation or is my way of obtaining
>> snapshots wrong?
>>
>>
> The molecule isn't fragmented, it's just split across periodic boundaries.
> trjconv can take care of that too (see trjconv -h).
>
>  Also, there was another question, I wanted to know how the geometry is
>> preserved in the average structure as computed by gromacs?The average
>>
>> structure calculated during analysis would be the average of all the
>> atomic
>> positions/co-ordinates during the length of simulation. But, I wanted to
>> know how are the bond angles treated for computation of the average
>> structure? Since, we use the structure for further analysis too. Are the
>> bond lengths distorted or they are retained while average is being
>> computed? Also, what are the co-ordinates used for this computation?
>>
>>
> http://www.gromacs.org/**Documentation/Terminology/**Average_Structure<http://www.gromacs.org/Documentation/Terminology/Average_Structure>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Ankita Naithani