On 26 August 2011 12:06, Justin A. Lemkul <jalem...@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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Thanks, J. N.
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