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

[Juliette N.]

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.
>
>


> -Justin
>
>  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
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Thanks,
J. N.
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