AMBER Archive (2008)

Subject: AMBER: "Assuming uniform neutralizing plasma"

From: Evan Kelly (
Date: Tue Feb 26 2008 - 20:01:52 CST

Hi Everyone,

Recently, I ran a short test job in sander (v9). It was a small
molecule with a +1 molecular charge in a box of TIP3P water with no
explicit ions present. I noticed that the sander output included a

"Assuming uniform neutralizing plasma"

and I am hoping to learn more about this. My guess is that this is
done to avoid infinite energies of a periodic system with a charged
unit cell, but I would like to know HOW it is implemented and learn
about any potential shortcomings or cautions in performing simulations
that use this "neutralizing plasma".

My specific interests are in performing MD simulations on small
molecules that may have 0, +1, or -1 molecular charges. These
simulations should be run in TIP3P water (ie. not in GB) to compare
with other simulations I have done of large systems. I would like to
keep the simulation boxes small (say 1000 water molecules) to keep
computational cost low, and I don't know if adding explicit ions makes
physical sense for such a small system.

I would greatly appreciate it if someone would share their thoughts on
the "neutralizing plasma".

Best Regards,

Evan Kelly

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