From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Thu May 10 2007 - 09:10:47 CDT
On Thu, 10 May 2007, Alessio Alexiadis wrote:
> Hi everybody
> I have a basic question. Water models (like TIP3P, SPC et.) usually are
> reported with the Lennard-Jones values of the oxygen-oxygen interaction.
> 1) What happens to hydrogen-hydrogen and hydrogen-oxygen interaction;
> are they neglected?
Those interactions are not really neglected, as there is a Coulombic
interaction between the H and O atoms that is quite strong (given by the
partial charges defined in the topology file). In general, hydrogens bonded
to an oxygen or nitrogen are frequently represented as a point charge
without any corresponding Lennard-Jones (dispersive) parameters. This
works as long as the rest of the force field is parameterized accordingly.
> 2) If they are not neglected, why they did not appear in literature?
> 3) If they are actually neglected, why in some NAMD tutorials (the one concerning CNTs for instance) there is?
> HT -0.046000(epsilon) 0.224500(Rmin/2)?
I don't know the history of TIP3P, but it seems that a small LJ component
has been added to the force field in a attempt to improve it's
reproduction of some physical properties.
Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)577-3810
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