From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] kappa in Generalized reaction field
Date: Mon, 15 May 2006 11:52:12 +0200
Berk Hess wrote:
From: Tomoshi Kameda <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: [gmx-users] kappa in Generalized reaction field
Date: Mon, 15 May 2006 17:28:27 +0900
Hi all
I'm going to ask about the definition of kappa in Generalized
Reaction-field.
In manual-3.3.pdf and manual-3.2.pdf (eq 4.17),
kappa**2 = ...SUM (c_i * z_i)
But, in Ref.51 (eq 5),
kappa**2 = ...SUM (c_i * (z_i)**2)
Is eq.4.17 correct?
I would say the reference is correct.
David van der Spoel removed the square from the code in 1999,
I don't know why.
It says in the code:
/* Changed from square to fabs 990314 DvdS
* Does not make a difference for monovalent ions, but doe for
* divalent ions (Ca2+!!)
*/
OK, I checked it in Atkins, Physical Chemistry, and it should be squared,
so the code and manual are incorrect. The code is incorrect for multivalent
ions only I think.
I think not.
There is an additional factor of 2 in the code.
I = 1/2 sum c_i Z_i
This half is correct in the formula in the manual, but not in the code.
Do we want to keep this code at all?
Good question.
I think simulating ionic solutions with reaction-field causes large
artifacts,
unless the concentration is very high and the cut-off quite long.
PME is a much better choice.
On the other hand it does not cost much code overhead,
just the formula.
Berk.
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