Re: about counterions

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 20 2006 - 10:07:29 CST

As a side note, if you're using Ewald based electrostatics (like PME),
you also need to have a neutral unit cell, as otherwise you're summing
over infinitely tiled charged cells.
Peter

Mark Abraham wrote:
> taojinwuhan_at_sohu.com wrote:
>
>> Hi, all
>>
>> In MD we always add counterions to neutralize protein, but I doní»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 caní»t be equilibrated in a
>> long time. Does anybody meet similar situation?
>>
>
> Not by design :-)
>
> Mark
>

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