AMBER Archive (2004)

Subject: Re: AMBER: PBC in sander

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 31 2004 - 22:57:49 CDT

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.

...dac
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