Re: [AMBER] how critical charge neutralization of a system

From: Jason Swails <>
Date: Fri, 25 Mar 2011 15:39:52 -0700

If the ions are only there to preserve net charge neutrality, then PME has a
'net neutralizing plasma' effect induced by the way the summation is

Tom Cheatham had a nice post about this a couple years ago: . If
explicit ions are crucial to the system dynamics, then this will obviously
not capture that. However, it does prevent the energies from diverging and
gives reasonable results.

Others' comments/opinions may be forthcoming ;).

Good luck,

On Fri, Mar 25, 2011 at 2:02 PM, Mahmoud Soliman <>wrote:

> Dear Amber users
> How serious if I forgot to neutralize the total charge of my system
> (enzyme
> -ligand complex)???
> Best wishes
> Mahmoud
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Mar 25 2011 - 16:00:03 PDT
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