AMBER Archive (2009)

Subject: [AMBER] solvent and counter ions

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Mar 04 2009 - 15:36:36 CST

forgive the generality of this question,

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.

Thank you,
Taufik

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