Mark Abraham wrote:
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 ).
This is not strange at all. These force fields are probably optimized to
achieve different targets under different simulation conditions on a
different test set. There is no wonder that they are different, and
there's no particular expectation of correlation with any property of
real Na+. Ensemble average properties of systems with solvated Na+
should be reasonable, however.
So I just want to know how the
developers of gmx or gromos force field get Lennard-Jones parameters for
Na+.
You should find the original literature that describes them and read it.
That's why the authors wrote it :-)
@article{Hermans84,
author = {J. Hermans and H. J. C. Berendsen and W. F. van
Gunsteren and
J.
P. M. Postma},
title = {A consistent Empirical Potential for Water-Protein
interactions
},
journal = {Biopolymers},
year = {1984},
volume = {23},
pages = {1513-1518},
}
@Article{Oostenbrink2004a,
author = {Chris Oostenbrink and Alessandra Villa and Alan E.
Mark and
Wilfred F. {Van Gunsteren}},
title = {A Biomolecular Force Field Based on the Free Enthalpy
of Hydra
tion and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6},
journal = {J. Comp. Chem.},
year = 2004,
volume = 25,
pages = {1656-1676}
}
@book{gromos96,
author = {W. F. van Gunsteren and S. R. Billeter and A. A.
Eising and P.
H.
H{\"u}nenberger and P. Kr{\"u}ger and A. E. Mark and W. R. P. Scott
and I. G. Tironi},
title = {Biomolecular Simulation: The {GROMOS96} manual and
user guide},
year = {1996},
address = {Z{\"u}rich, Switzerland},
publisher = {Hochschuleverlag {AG} an der {ETH} {Z}{\"u}rich}
}
Now please don't think that there will be any information about the ion
parameters in any of these papers. If you want to know whether ANY salt
force field is ANY good, maybe you should read this instead:
@article{Hess2006c,
author = {B. Hess and C. Holm and N. van der Vegt},
title = {Osmotic coefficients of atomistic NaCl (aq) force fields},
journal = {J. Chem. Phys.},
year = {2006},
volume = {124},
pages = {164509},
optabstract = {Solvated ions are becoming increasingly
important for (bio)molecular
simulations. But there are not much suitable data to validate the
intermediate-range solution structure that ion-water force fields
produce. We compare six selected combinations of four biomolecular
Na-Cl force fields and four popular water models by means of
effective
ion-ion potentials. First we derive an effective potential at high
dilution from simulations of two ions in explicit water. At higher
ionic concentration multibody effects will become important. We
propose
to capture those by employing a concentration dependent dielectric
permittivity. With the so obtained effective potentials we then
perform
implicit solvent simulations. We demonstrate that our effective
potentials
accurately reproduce ion-ion coordination numbers and the local
structure.
They allow us furthermore to calculate osmotic coefficients that
can be directly compared with experimental data. We show that the
osmotic coefficient is a sensitive and accurate measure for the
effective
ion-ion interactions and the intermediate-range structure of the
solution. It is therefore a suitable and useful quantity for
validating
and parametrizing atomistic ion-water force fields. (c) 2006
American
Institute of Physics. 0021-9606}
}
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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