RE: Avoiding Rotation and translation of protein

From: Blake Charlebois (
Date: Wed Jun 08 2005 - 12:39:06 CDT

The following thread may help:

There are several related (and possibly more useful) threads. You can find
them with a Google search specifying namd-l as one of the search terms.

You should read the section of the NAMD manual on wrapping coordinates. You
may find some useful scripts on the VMD site for reversing coordinate
wrapping in a dcd file.

Does your protein consistently rotate in the same way? Does it have a large
dipole moment? If so, you may want to increase your box size.


-----Original Message-----
From: [] On Behalf
Of Leonardo Sepulveda Durán
Sent: June 8, 2005 11:59 AM
Subject: namd-l: Avoiding Rotation and translation of protein


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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