AMBER Archive (2000)

Subject: Re: About PME neutralization

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Mar 08 2000 - 12:40:41 CST

yes indeed that is how the charge is neutralized
Tom D

On Mon, 6 Mar 2000, [iso-2022-jp] 渡辺克博 wrote:

> Hi AMBER users.
>
> I think a neutralization of a system containing a protein is a VERY VERY
> important problem. So I want to know the meaning of next statements.
>
> --------------------------------------------------------------from Manual
> ISCHARGED
> Standard use is to have ISCHARGED = 0
> which forces neutralization of the unit
> cell by removal of the average charge over
> the system at the beginning of the run.
> [This is necessary due to the roundoff
> error associated with the parm derived
> charges (upon reading in a parameter file,
> the sum of the charges for a neutral sys-
> tem does not sum to zero).] When
> ISCHARGED = 1, the unit cell is not neu-
> tralized. Technically, the Ewald summa-
> tion method is not correct when a non-
> neutral system is used (energy will
> change, independent of the direct sum tol-
> erance, but the forces are still correctly
> determined). However, the method has been
> applied for non-neutral systems and may be
> useful for equilibrating systems in the
> absence of counterions, for example.
> ---------------------------------------------------------------------------
>
> Does
> 'by removal of the average charge over the system at the beginning of
> the run'
> mean
>
> "
> average = sum_of_charge / natom
> do i=1,natom
> charge(i) = charge(i) - average
> enddo
> "
> ?
>
> thank you.
>
> katsuhiro watanabe
> Hitachi ULSI Systems. Co.ltd
>