[gmx-users] Interaction energy

[Nick Johans]

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?

So what about PMF. It seems like an interaction energy too, but more
accurate one???

>
> -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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>