[gmx-users] Coulomb and vdW energies

[Shreyas Kaptan]

Hi.

I would not say that it is completely unrealistic/unphysical. Especially,
the Electrostatic part. If within two subgroups, you could show that there
is systematic repulsive or attractive potential, that could lead to some
hypothesis about how they interact (e.g. pushing/pulling). Of course, this
is only true of ratios of decomposed energies that are large proportions of
the total energy, as smaller portions might not be really
significant indicators of strong interactions.

Shreyas

On Sat, Nov 30, 2019 at 6:47 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/30/19 3:14 AM, elham wrote:
> > Dear all, I want to obtain the coulomb and vdW energies between two
> atoms of separate molecules, However  the .edr output calculate coulomb
> and vdW energies of whole system. There is not any option(like -n .ndx) to
> define the the special atoms in the gmx energy command. How can I calculate
> the coulomb and vdW energies between the two atoms which are related to two
> separate molecules?Best
>
> Set energygrps in the .mdp file, generate a new .tpr, and use mdrun
> -rerun to re-evaluate the energies from an existing trajectory. Note
> that decomposition of energy in this way has no physical meaning. Total
> interaction energy may be physically realistic if the force field was
> specifically parametrized against e.g. QM target data but decomposing
> the energy in this way is not meaningful.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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>
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-- 
Shreyas Sanjay Kaptan