[gmx-users] Interaction energy

Justin Lemkul jalemkul at vt.edu
Mon Nov 26 18:58:18 CET 2018

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?


> 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.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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