[gmx-users] LJ-14 / LJ(SR)

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 26 18:06:09 CEST 2011

Juliette N. wrote:
> Hello everyone,
> I know the following question has been discussed many times in the 
> archive but unfortunately I am still unclear about it therefore I would 
> like to ask for your patience.
> I am interested in non bonded interactions, i.e LJ(SR) and it has been 
> said that LJ-14 potentials are /inter/molecular non bonded interactions. 

1-4 interactions are intramolecular, occurring between atoms separated by 3 
bonds.  They are not intermolecular.

> This definition confuses me as I can't figure whether they have to be 
> added up to LJ(SR) (which as I understood correctly contains bonded 1-5, 
> 1-6,... interactions + all nonbonded interactions between atoms of 
> different molecules within Rc), or they are treated bonded interactions 
> and must not be added to LJ(SR). I would like to get a clear idea of the 

The LJ-14 term is a nonbonded term.


> nature of these types of interactions which I can't realize from the 
> term '/inter/molecular non bonded interactions".
> Please briefly shed some light on this.
> Thanks,
> J.


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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