From: Robert Brunner (rbrunner_at_illinois.edu)
Date: Fri Aug 07 2009 - 12:03:50 CDT
Periodic boundary conditions mean that the system is replicated
periodically, so it wraps around on itself, and atoms feel forces do
the images of the system. This is the most common mode.
Spherical boundaries allow you to specify a spherical force field
around you simulation. Atoms that drift into the shell feel a force
opposing them moving further out. Cylindrical boundaries are the same
except the shell is a cylinder.
Most simulations use periodic boundary conditions.
On Aug 7, 2009, at 11:04 AM, Aurum Bai wrote:
> Hello, everyone
> I found there are "periodic boundary","spherical harmonic boundary"
> and "cylindrical harmonic boundary conditions" in namd simulation.
> But I do not what are they different?
> Who can tell me what are the different between them, or how to
> choose them in some conditions?
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