Re: [gmx-users] Re: LJ

>Thank you so much for your explanation. I am just guessing in the last >statement you meant *inter* molecular! Yes. INTERmolecular, between chemically nonbonded particles. >> >> Formally, you can kill this energy by going to the main topology file >> (like ffgmx.itp) and setting FudgeLJ term to

Re: [gmx-users] Re: LJ

Dr. Vitaly V. Chaban wrote: Hi Juliette, Formally, you can kill this energy by going to the main topology file (like ffgmx.itp) and setting FudgeLJ term to zero, although I think that you don't actually want to do so. LJ-14 is the energy between the atoms belonging to the SAME molecule, so if

Re: [gmx-users] Re: LJ

Hi Juliette, Formally, you can kill this energy by going to the main topology file (like ffgmx.itp) and setting FudgeLJ term to zero, although I think that you don't actually want to do so. LJ-14 is the energy between the atoms belonging to the SAME molecule, so if you consider e.g. heat of vapori

Re: [gmx-users] Re: LJ

On 26 August 2011 15:17, Justin A. Lemkul wrote: > > > Juliette N. wrote: > > >> >> On 26 August 2011 13:25, Dr. Vitaly V. Chaban > vvcha...@gmail.com>> wrote: >> >> >>. Now it is clear that >> >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded >>potentials. Thank >> >>

Re: [gmx-users] Re: LJ

Juliette N. wrote: On 26 August 2011 13:25, Dr. Vitaly V. Chaban > wrote: >>. Now it is clear that >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. Thank >> you so much. The answer actually depends on what you call "

Re: [gmx-users] Re: LJ

On 26 August 2011 13:25, Dr. Vitaly V. Chaban wrote: > >>. Now it is clear that > >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. > Thank > >> you so much. > > The answer actually depends on what you call "nonbonded potential". If > you want to calculate e.g. the interact