AMBER Archive (2009)
Subject: Re: [AMBER] solvent and counter ions
From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Mar 05 2009 - 17:29:50 CST
> Thank you Thomas for clarifying this. Is it acceptable to add counter
> ions first and then water (solvent)? and then allow the solvent-ions to
> relax in an initial minimization where the solute is fixed? (avoiding
> the process of selecting and deleting water molecules)
You will get less optimal packing - the ions will be placed on
points of a 1A grid and waters will be subtracted from the water
box accordingly during the solvation process. I.e. fewer waters
are deleted when addions after solvate. addions then solvate means
more vdw voids and thus lower initial density of the system.
FWIW, I wrote the code for doing it both ways.
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