[gmx-users] Re: LJ

Juliette N. joojoojooon at gmail.com
Fri Aug 26 21:12:04 CEST 2011

On 26 August 2011 13:25, Dr. Vitaly V. Chaban <vvchaban at gmail.com> 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 interaction energy between two
> molecules, then you should NOT include this term.

Thank you for you reply. I am actually interested in interaction energies
(cohesive energy between particles which is related to enthalpy of
vaporization) and noticed that inclusion of this term results in far less
accurate results. The net energy is of repulsion type and adding a positive
term ( LJ-1-4) makes my results inaccurate.  I am already using nexcl = 3 in
the topology which means 1-5, 1-6 neighbors are accounted for. But still LJ
-1-4 is appearing. So far I have been ignoring this term (energy value) in
my calculations, but my concern is that by just neglecting this energy term
(value) I am not ignoring the actual effect of a potential term on the
physics of the system. Is there any way to switch off this term?


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