[gmx-users] a residue move in extremely large scale in MD

Justin Lemkul jalemkul at vt.edu
Sat Aug 11 02:02:56 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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