[gmx-users] regarding calculation of intra-residue energy

[Justin Lemkul]

On 12/26/17 1:34 PM, Saumyak Mukherjee wrote:
> Dear all,
>
> I have simulated myoglobin in water system. Now, I want to calculate the
> self interaction energy (Coulomb) of the protein. In that case shall I
> consider the interaction between the OE1 and OE2 atoms in glutamte, or
> other such pairs?
>
> Including all pairs, except the bonded pairs, the average self-energy of
> the protein is coming as 8108 kT from my program. Is this value plausible?
>
> Any comment/suggestion is appreciated.

First- and second-neighbor interactions are not included in standard 
force fields, so if your calculation includes them, you're going to get 
something that the force field is not designed to describe. Use the same 
exclusions as the force field expects.

-Justin

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

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