Subject: van der Waals parameters

From: [email-masked] (Bill Ross )
Date: Wed, 8 Dec 1993 16:13:16 -0800

From: "Tahmid I. Mizan" <[email-masked]>

	I address my question (probably a trivial question) to any obliging 
	molecular dynamics guru:

Perhaps I'm not a guru, but here's what I know:

  Van der Waals interactions are parameterized by Lennard-Jones (L-J) 
  '6-12' potentials of the form
	
        E = AiAj/r^6 - BiBj/r^12

  where A and B parameters for the types of atoms i and j are derived for 
  the potential between two atoms of the same type. This same-type potential 
  curve can also be defined by the radius  (r *) corresponding to half the 
  internuclear distance at the point of minimum energy, and the potential 
  well depth ('e') at that internuclear distance. In this convention the 
  potential energy for the van der Waals interaction between atoms 'i' and 'j' 
  is defined as (r*ij, eij), where r*ij is (r*i + r*j), and eij is 
  sqrt(eiej). This is the convention which is used by AMBER.

So sigma is the internuclear distance at the potential minimum for 
two atoms, corresponding to R*ij. R* for a single atom corresponds
to the sound of one hand clapping, in that it can mislead one to
think that if the universe consisted of a single atom, that atom
would have a size.

Bill Ross