AMBER Archive (2008)

Subject: AMBER: reg.concentration of ions

From: balaji nagarajan (
Date: Fri Dec 12 2008 - 10:34:49 CST

dear amber .,

I am not aware of the concentration of ions added to the water box
in the dynamics
how to add a particular concentration of ions in
it ., ?
actually before running dynamics
the charge should be neutral
so if i wish to add Mg then i have to neutralise it with some -ve charge
but what about adding sodium in dna to neutralize ... and if i want some more ions
i have to do it again
am i right ?
thanks in advance

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