[gmx-users] Interaction energy

Justin Lemkul jalemkul at vt.edu
Mon Nov 26 19:37:44 CET 2018

On 11/26/18 1:35 PM, rose rahmani 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?
>>> 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.
> If interaction energy between protein1 and special ligand is more than
> between protein2 and that ligand, it is tru its free energy would also be
> more than it?

No, because you know nothing about desolvation penalty and loss of 
entropy upon binding.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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