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.
Do we want to keep this code at all?
Also in the code there is an additional factor of 2.
But with charged groups in solution I would stongly advise
against using a (generalized) reaction field, as this can produce
strong artifacts.
Use PME instead.
Berk.
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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