AMBER: PBC in sander

From: Mingfeng Yang <>
Date: Tue, 31 Aug 2004 16:27:26 -0400

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!

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Received on Thu Sep 02 2004 - 01:15:12 PDT
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