AMBER Archive (2009)

Subject: Re: [AMBER] Xleap - solvatebox - counterions

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jan 30 2009 - 12:40:07 CST

> If I solvate (solvatebox test TIP3PBOX 10) my molecular system previously
> neutralized with Na+ counterions

By the way it is better to solvate then addions, because then each
ion replaces a single water.

Other than that, you have found an interesting case. The larger size of
K+ vs. Na+ might mean that K+ is placed further from the solute and this
in turn expands the box for subsequent solvation.

Bill

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