[gmx-users] Interaction energy
johans.nick93 at gmail.com
Mon Nov 26 16:51:50 CET 2018
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
> > 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?
If coulomb energy is also existed between pairs, so the interaction energy
will be LJ+Coulomb yes?
So what about PMF. It seems like an interaction energy too, but more
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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