[gmx-users] kappa in Generalized reaction field
David van der Spoel
spoel at xray.bmc.uu.se
Mon May 15 11:52:12 CEST 2006
Berk Hess wrote:
>> From: Tomoshi Kameda <kameda-tomoshi at aist.go.jp>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: gmx-users at 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
>> 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.
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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