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

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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