[gmx-users] kappa in Generalized reaction field
gmx3 at hotmail.com
Mon May 15 12:00:53 CEST 2006
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at 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 <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
>>>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.
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?
I think simulating ionic solutions with reaction-field causes large
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.
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