[gmx-users] Re: LJ

Dr. Vitaly V. Chaban vvchaban at gmail.com
Fri Aug 26 19:22:37 CEST 2011

>>> 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.

I guess they are non-bonded because these atoms are not directly
bound. They are separated by 3 chemical bonds, yet belonging to the
same molecule.

Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216

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