[gmx-users] Re: The Lennard-Jones parameter of Na+? (Mark Abraham)

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 10 09:08:26 CEST 2007

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 :-)

         author = {J. Hermans and H. J. C. Berendsen and W. F. van 
Gunsteren and
         P. M. Postma},
         title = {A consistent Empirical Potential for Water-Protein 
         journal = {Biopolymers},
         year = {1984},
         volume = {23},
         pages = {1513-1518},

   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}

         author = {W. F. van Gunsteren and S. R. Billeter and A. A. 
Eising and P.
         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:

         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 
         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 
         to capture those by employing a concentration dependent dielectric
         permittivity. With the so obtained effective potentials we then 
         implicit solvent simulations. We demonstrate that our effective 
         accurately reproduce ion-ion coordination numbers and the local 
         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 
         ion-ion interactions and the intermediate-range structure of the
         solution. It is therefore a suitable and useful quantity for 
         and parametrizing atomistic ion-water force fields. (c) 2006 
         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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list