[gmx-users] LJ-14 / LJ(SR)
joojoojooon at gmail.com
Fri Aug 26 18:15:44 CEST 2011
On 26 August 2011 12:06, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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.
Sorry, that was my mistake. I meant intra/ molecular nonbonded. Thats is why
I was wondering if I have to add up to LJ SR or not. Now it is clear that
the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. Thank
you so much.
> 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.
> 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
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