Re: AMBER: PBC in sander

From: David A. Case <>
Date: Tue, 31 Aug 2004 20:57:49 -0700

On Tue, Aug 31, 2004, Mingfeng Yang wrote:
> 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

Sander makes no distinction between "solute" and "solvent" atoms. Periodic
conditions replicate all atoms, of whatever "type" they are.

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