From: Ashar Malik (
Date: Wed Nov 12 2014 - 00:41:23 CST


Looking at the system - wanted to add two things.

1) Since the cubic box indicates the periodic boundaries - the chain is
pretty close to the boundary at the start. That is not good since you need
to have significant margin from the boundaries, which should be fairly
equal on all sides. Otherwise it will mess up your electrostatic
calculations (with the cutoff and everything).

2) What I said earlier was that you can control that the coordinates wrap
only when all of the atoms of the chain have moved out of the system. You
can control this by turning on wrapALL and wrapNearest in your NAMD
configuration file. This way only when the entire chain has moved out of
one side will it be wrapped around the boundaries.