[gmx-users] Interaction energy

[rose rahmani]

On Mon, 26 Nov 2018, 21:28 Justin Lemkul <jalemkul at vt.edu wrote:

>
>
> On 11/26/18 10:51 AM, Nick Johans wrote:
> > On Mon, 26 Nov 2018, 18:22 Justin Lemkul <jalemkul at vt.edu wrote:
> >
> >>
> >> On 11/22/18 11:41 AM, Nick Johans wrote:
> >>> Hi
> >>>
> >>> I am beginner in MD. Maybe it is not a wise question but i want to
> >>> calculate the interaction energy between protein and ligand and also
> PMF
> >> in
> >>> different distances. But i don't know what is the didference between
> >> PMF, i
> >>> mean free energy in particular(by umbrella sampling) and the
> interaction
> >>> energy (by g_energy tool) in my case?
> >> Interaction energy is a pairwise decomposition of short-range nonbonded
> >> interaction energy in the system. This energy is usually not physically
> >> meaningful, but if the force field has been parametrized in such a way
> >> that it is, the interaction energy is a contribution to the enthalpy of
> >> the system.
> >>
> > What forcefields embedded in GROMACS do, yes?
>
> AFAIK only CHARMM.
>
> > If coulomb energy is also existed between pairs, so the interaction
> energy
> > will be LJ+Coulomb yes?
>
> Pairs are 1-4 (intramolecular) interactions, so if you define
> interaction energy between two nonbonded species, you'll get zeroes for
> all the pair energies, by definition.
>
> > So what about PMF. It seems like an interaction energy too, but more
> > accurate one???
>
> That's not what a PMF is. A PMF is the change in free energy of a system
> as a function of progress along a reaction coordinate.
>
If interaction energy between protein1 and special ligand is more than
between protein2 and that ligand, it is tru its free energy would also be
more than it?

>
> -Justin
>
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> Assistant Professor
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