[gmx-users] Interaction energy

[Mark Abraham]

Hi,

On Mon, Nov 26, 2018 at 7:47 PM Nick Johans <johans.nick93 at gmail.com> wrote:

> 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.
> >
> Interesting! You mean interaction energy calculated by for example AMBER
> may not be true? Why?? What makes CHARMM unique??
>

As Justin said, the difference is in the way it is parametrized.
Forcefields are generally built to be additive, but it does not follow that
they are decomposable.

> > 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.
> >
> It's exactly the SR(short range) selection in g_energy, yes?


You seem to be using a looser definition of pairs than is usual in
discussion of GROMACS topologies.


> all long range
> are zero.


If there's a long-range model, then such interactions are not uniformly of
zero magnitude...


> But coulomb and LJ are non-zero. So, in this case the interaction
> energy would be
> Short range LJ+ Short range Coulomb , true?
>

As far as I'm concerned, you can invent whatever quantity you want, but the
burden is on you to demonstrate that there's a reason to connect it to
something physical.

Mark


> >
> > > 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.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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