Re: Interaction energy definition

From: Aron Broom (
Date: Sat Nov 23 2013 - 07:09:54 CST

yes the potential will be from whichever forcefield is used in the NAMD
config file.

you'll need to be very careful about comparing to a solvation enthalpy. In
your original email you mention this lattice. You can't calculate the
deltaH without a reference like this. Comparing against a vacuum (H = 0
for the pair interactions) isn't really meaningful. Rather you need to
compare against a lattice of proteins all interacting with one another with
no solvent.

So if the enthalpy from the pair interaction is high or low, that doesn't
actually mean anything without comparing it to the lattice.


On Fri, Nov 22, 2013 at 4:21 PM, nan li <> wrote:

> Thank you for your reply, Aron.
> As I specified Amber force field, the interaction energy between
> peptide-water is derived from Amber potential, right? You mentioned
> pairwise interaction energy is corresponding to solvation enthalpy. Is it
> right to say if interaction energy is low (or high), then solvation
> enthalpy is low (or high)?
> Thank you.
> 2013/11/22 Aron Broom <>
>> The interaction energy is the sum of all the pairwise potentials that
>> would be calculated when doing MD. So for water and protein that will be
>> the sum of all the pairwise VDW, and electrostatic terms between all pairs
>> of water-protein atoms.
>> Since that interaction energy in a vacuum would be 0, I suppose you can
>> make the argument that there is some relation to the solvation enthalpy,
>> but the problem is that you're ignoring any changes in protein-protein
>> enthalpy that might happen as a result of being solvated.
>> Anyway, the main point here is that the interaction energy is very
>> precisely defined in terms of forcefield potentials, but interpreting what
>> that means is something else.
>> On Fri, Nov 22, 2013 at 3:45 PM, nan li <>wrote:
>>> Hi all,
>>> I am using pair interaction energy calculation to get the "interaction
>>> energy" between water and protein in a system. I am confusing about the
>>> definition of "interaction energy". Is it the enthalpy of solvation?
>>> DeltaH= Delta H{lattice energy} + Delta H {solvation}.
>>> or is the "interaction energy between water and protein" the mixing
>>> enthalpy DeltaH?
>>> Also, if the interaction energy is for protein-ligand interaction, is
>>> the interaction energy the mixing enthalpy?
>>> Many thanks.
>>> Nan
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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