On 7/10/2007 2:53 PM, Hu Zhongqiao wrote:
Dear Mark
Thanks for your reply.
In more detail, I used ffg43a1 force field. In the file ffG43a1nb.itp,
one can find the Lennard-Jones parameters for Na+ as follows:
C6=7.2063121e-05; and C12= 2.1025e-08
>From these 2 values one can get epsion(Na+)=0.0617 kJ/mol.
Because the force field parameters for ions is relatively simple, the
main interaction of Na+ with other particles is electrostatic and van
der Waal's forces. And I also believe that the combination rule makes
not big difference for different force fields in this case. It is
strange epsion(Na+) = 0.0617 kJ/mol in ffg43a1 is very different from
some references (for example, in the paper shown in my last email, this
value is epsilon(Na+) = 0.42 kJ/mol ). So I just want to know how the
developers of gmx or gromos force field get Lennard-Jones parameters for
Na+.
They are never simple and tends to be problematic. The recent concern
over abnormal clustering of excess K/Na with Cl in AMBER force field has
highlighted the need of better parameterization of ions. A short
description of this problem is on page 5 of
Auffinger, P., Hashem, Y. Nucleic Acid Solvation: from outside to
insight, Current Opinion in Structural Biology, 2007 17:1-9
Back to your problem, you may dig the literature about the root of these
two set of parameters.
Zhongqiao
Dear all,
I find the Lennard-Jones parameter epsilon of Na+ in Gmx is very
different from some references.
In gmx, I calculated sigma(Na+)=0.258nm, epsilon(Na+)=0.0617 kJ/mol
But many researchers cited a paper by Dang LX [J. Am. Chem. Soc.,
1995,
117, 6954-6960] and used parameters as follows sigma(Na+)=0.258nm,
epsilon(Na+)=0.42 kJ/mol.
I want to ask where parameter of Na+ in gromos force field comes from?
Is it reasonable?
In isolation, no force field parameter has any meaning. See
http://wiki.gromacs.org/index.php/Force_Fields#Usage
Mark
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