[gmx-users] Re: Lennard-Jones Interactions in Gromacs

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 2 21:23:47 CET 2012

Lara Bunte wrote:
> Please help :-(

Please realize that you're asking for free help from a global mailing list.  You 
may not get a reply from someone immediately, as that person may be busy with 
their own work, or even asleep ;)

 From your original post:

 > In a supporting Information of a paper is written:
 > "The description of the LF radical force fields is complete, as soon as also
 > the parameters of the Lennard-Jones potentials are given. For these parameters
 > we adopt the values specified in the CHARMM22 force field for the basic atom
 > types"
 > Please tell me how, what and where I have to do this.
 > I know that Lennard-jones interactions are in the ffnonbonded.itp file in the
 > section [ pairtypes ]but I don't know what

The [pairtypes] directive is for adding special 1-4 interactions.  Everything 
else is simply stated in the [atomtypes] directive, providing sigma/epsilon or 
C6/C12 parameters, whatever is required by the force field.  L-J interactions 
between different atom types are then generated according to combination rules. 
  Some force fields (like Gromos) use additional [nonbond_params] for 
interactions that do not follow standard combination rules, but that's not 
necessarily relevant here.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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