AMBER Archive (2009)
Subject: Re: [AMBER] solvent and counter ions
From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Mar 04 2009 - 18:20:45 CST
> In literature, after water (solvent) is added few water (solvent)
> molecules are removed and replaced by counter ions, what is the reason
> behind this? is it incorrect to add solvent and counter ions without
> removing any solvent atoms?
> i just want to know if the problem is having an ion placed too close to
> a water molecule? or if the density is affected somehow? if this has
> been discussed somewhere, a link to the discussion would help me as well.
If you place an ion so that 4 waters need to be removed to avoid
steric overlap, there is much more vdw void created than if you
place the ion directly over one water. The more vdw voids to fill
by constant-pressure equilibration, the smaller your system will
be when equilibrated.
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