Avoiding Rotation and translation of protein

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Wed Jun 08 2005 - 10:58:33 CDT


I am performing a NPT dynamics of a protein. I use a 10A waterbox, and
2 ions (neutral system), PBC and PME. At 400 ps, the protein begins to
rotate (I dont Know if its center of mass translates too),
furthermore, one residue comes dangerously close to the border of the
box. I would like to ask if there is a way to avoid such protein
movements in the simulation, or whether there is a way to reorganize
trayectory files later in order to obtain a dcd where this movements
are taken out. And if that is posible, what happens if one of my
protein's residue steeps through th boundary? Is that Dynamics lost???


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