From: Hai Long (spaceshiptoo_at_gmail.com)
Date: Fri Nov 30 2007 - 11:09:35 CST
Hi:
I'm intersted in this question too. As far as I know, a charged system
under PME will result in a infinite energy, obviously this is not the
case for NAMD. For charged system, Amber will apply a
uniformly-distributed charge cloud to the whole box in order to
neutralized the system. Is NAMD using a similiar approach? By the way,
I suggest that NAMD should print a big warning message in the output
when the system is not neutral.
Hai
> From: Richard Swenson (swenson_at_hec.utah.edu)
> Date: Thu Nov 29 2007 - 14:53:18 CST
>
>
> I recently made a mistake in one of my bilayer simulations and left out the
> counter ions. The result was a system with a net -21e charge. I was able
> to run over 10ns of dynamics without any problems, but wonder how NAMD
> handles PME on a charged system. Could someone point me to information on
> this?
>
> Thanks in advance,
>
> Richard
>
>
> Ps. I do not plan to use these simulations due to the net charge.
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