On 8/10/12 7:58 PM, Acoot Brett wrote:
Dear Dr. Dallas Warren,
My protein is a protein-peptide complex. The residues I mentioned which moves
in a large scope is from the peptide, it is the last 3rd residue of the
peptide, a lysine.
I compared this lysine position with the other residue positions (including the
peptide binding pocket and the all the peptide residues) with PDB from
different time intervals (total MD is 10 ns, and I extracted the PDB every 0.5
ns, and then I align all the PDB files and compared the relative position of
this lysine in different PDB files), I find this lysine position changed most
significantly during the whole 10 ns MD.
Quantitative analysis is more convincing - RMSD, RMSF, etc.
In addition, will you please tell me how to analysis whether the phenomenon is
from periodid boundary effect? I have no knowledge on how boundary effect
affect the MD.
Center the system with iterations of trjconv, i.e. trjconv -pbc mol -ur compact
followed by trjconv -center. If the outcome of the analysis before and after
PBC correction are the same, then you can rule out PBC effects, though they
should be fairly obvious upon watching the trajectory anyway.
-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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