[gmx-users] interaction energy
jalemkul at vt.edu
Mon Feb 24 19:15:46 CET 2014
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
> 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 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
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