AMBER Archive (2009)

Subject: Re: [AMBER] implicit and explicit simulation: salt effect

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Jan 10 2009 - 10:26:45 CST

On Fri, Jan 09, 2009, David LeBard wrote:

> As far as I know, there is no parameter describing the Debye screening
> length for ions added to explicit solvent simulations. From this
> perspective, the effect of adding an ion (or increasing the salt
> concentration) to a real solution is mostly missing in explicit MD
> simulations because an MD ion cannot screen the electric field arising
> from the other charges in the simulation due to the lack of a Debye
> length parameter. Therefore, it is my understanding that MD ions in
> explicit solvent simulations are simply there to create the necessary
> zero net system charge needed for the Ewald summation.

I don't agree with this. The screening length is the result of the
microscopic motions of ions in water ... you don't need to input it into
the (explicit) calculation. There are lots of studies of salt-dependent
effects (in DNA and elsewhere) using explicit solvent/ion simulations.
An explicit screening length is appropriate when you don't have explicit
ions, as in GB simulations.

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber