AMBER Archive (2004)

Subject: AMBER: PBC in sander

From: Mingfeng Yang (
Date: Tue Aug 31 2004 - 15:27:26 CDT

Hi, fellows,

Is the periodic boundary condition applied to the solvent only, or also
the solute? Like a protein in a water box, do the image contains water
only or also the protein? And, when sander calculates the non-bonded
interaction, is the interaction between the protein and the
protein-image included? I learned that in some simulating software, they
only consider solvent in PBC. Thanks!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to