From: Axel Kohlmeyer (
Date: Wed Nov 12 2014 - 01:38:30 CST

On Wed, Nov 12, 2014 at 1:41 AM, Ashar Malik <> wrote:
> Hey,
> 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).

that statement is not quite correct. with periodic boundaries, it does
*not* matter where the protein is located in the box. the interactions
are for all practical purposes invariant against translation of the
system. however, it indeed *does* matter what the distance between
periodic images of the protein are. most people underestimate how much
space is needed for that, to keep the error within reasonable margins
(and even that is usually cutting it very, very close).


> 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.
> Best,
> /A

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.