Re: PME on a negatively charged system

From: Hai Long (
Date: Fri Nov 30 2007 - 11:09:35 CST


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.


> From: Richard Swenson (
> 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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