[gmx-users] Interaction energy

[Justin Lemkul]

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.

-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

==================================================