AMBER Archive (2000)

Subject: Re: PME with charged system

From: David Small (David.Small_at_hec.utah.edu)
Date: Tue Aug 15 2000 - 21:17:45 CDT

Marcela,

Sander and Gibbs (if that's what you're using) will neutralize the charge
at the beginning of the run, by applying the neutralizing factor across
all atoms so that the relative dynamics between atoms stay the same. I'm
not sure what kind of errors this introduces.

dave

On Tue, 15 Aug 2000, Marcela Madrid wrote:

> Hi
>
> Is there a way to use PME on a system that has a net charge
> of +1 ? What kind of error would that introduce?
> I am trying to calculate the difference in free energy between a neutral
> system and one with a charge of +1.
> thank you, Marcela
>