From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Tue Dec 19 2006 - 21:46:23 CST
taojinwuhan_at_sohu.com wrote:
> Hi, all
>
> In MD we always add counterions to neutralize protein, but I don’t
> understand it exactly. Why should we do that?
Usually a protein will have counter ions nearby in a real system, since
you'd have to do work to separate them, and biological systems tend to
be adapted not to do unnecessary work. For example, polarizing membranes
by moving ions around is expensive!
> What differences can be caused without counterions? Is there a
> reasonable explanation for adding counterions?
You may simulate something that has no relationship to reality if you
don't use appropriate counter ions.
> I try to run a MD without counterions, but it can’t be equilibrated in a
> long time. Does anybody meet similar situation?
Not by design :-)
Mark
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