[gmx-users] intermolecular energy

Jones de Andrade johannesrs at gmail.com
Sat Jun 23 09:18:10 CEST 2007

Hi Mark.

Haven't got exactly what you said. So let me rephrase myself:

The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic

What kind of contribution am I missing that makes potential energy minus
bond stretching minus angle bending *different* from Lj + coulomb(SR) +
coulomb (LR) + Disp correction?

Thanks a lot in advance,

Sincerally yours,


On 6/23/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > The intermolecular energy in the liquid should no be equal to the sum of
> > the
> > LJ, coulomb(SR, coulb(LR) and Disp Correction? And, that correct,
> > shouldn't
> > it be equal also to the potential energy minus bond minus angle bending
> > energies? What am I missing, that is making me have both different?
> Dunno since we can't read your mind about the sort of calculation you
> did... What does your logfile have?
> > Another question: what exactly is the "coul. recip." standing for? I
> > expected it had to be included in the above sums also, but the high
> values
> > it yelds would be nonsense.
> It's the reciprocal space sum of the Ewald method you're using. It sounds
> like you should read the section in chapter 4(?) of the manual that
> describes this. The reason it's large is that it has (roughly) all the
> long-range contributions from all of the atoms, and I don't think these
> can be sensibly broken down into by-atom components.
> So if you're interested in determining intermolecular energies, for some
> reason, you should design a simulation protocol that has a chance of doing
> this. In a GROMACS context, that probably means GRF electrostatics.
> Mark
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