[gmx-users] interaction energy

[Justin Lemkul]

On 2/24/14, 6:51 AM, maryam haji wrote:
> Dear gromacs users
>
> My system contains protein and CNT and water molecules.
>
> I want to obtain interaction energy. There is following equation in some
> papers:
>
> E(int) = E(cnt+protein) - E(cnt) - E(protein).
>
> Based on this equation, should 3 MD simulations?
>
> 1-  cnt in water
>
> 2- protein in water
>
> 3- protein and cnt in water
>
> I have 3 questions:
>
> 1) Is my opinion true?
>

No, 3 simulations are not required.

> 2) What means of E(x)? Are E(cnt) and E(protein) corresponded to total or
> potential energy
> of cnt and protein in simulation # 1 and 2?
>
> 3) Is E(cnt+protein) corresponded to total potential energy
> of cnt+protein in simulation #  3 ?
>

What those energy terms are indication are the potential energies associated 
with each component, including both intramolecular bonded and nonbonded terms.

Gromacs does the work for you if you specify energygrps in the .mdp file.  Note 
that when using PME, it is laborious to attempt to decompose the mesh term, and 
I'm not convinced it can be done so reliably.  Short-range nonbonded 
interactions are trivial to decompose in a pairwise fashion; this is what 
energygrps gives you.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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