[gmx-users] Snapshot and co-ordinate query

[Ankita naithani]

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

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?

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?

I would be really grateful if you could kindly guide me towards these
queries.

Kind regards

-- 
Ankita Naithani