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
--
========================================
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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