[gmx-users] Snapshot and co-ordinate query

[Justin Lemkul]

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

-Justin

-- 
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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

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