Questions tagged [binding-energy]

Questions related to the binding energy of a system, i.e., the amount of energy required to separate a particle from a system of particles or to disperse all the particles of the system, especially as it pertains to the atoms and ions bound together in crystals.

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8
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Binding energy calculation for Zn atom on armchair graphene slab?

I am trying to repeat the result of this paper for Zn absorbed on the armchair graphene slab. The relaxed top and side structures are the following: The relaxed structure is almost the same as the ...
9
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1answer
49 views

What is exfoliation energy per unit area?

I see in many sources the exfoliation energy defined with the unit $meV/A^2$ I frankly don't understand how it's calculated and I couldn't find any mathematical formula for that. its unit confuses me. ...
7
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1answer
77 views

Is it required to sample the full reaction coordinate in umbrella sampling?

Below is the free energy profile obtained after a histogram analysis of an umbrella sampling simulation. Generally, one is interested in the free energy difference (highest energy minus lowest energy)....
8
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2answers
92 views

Docked pose and energy minimization

Is it useful to energy minimize a docked pose before scoring it? I am speaking in the context of protein-ligand systems. Does the energy obtained after minimization correlate better with experimental ...
18
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2answers
130 views

Calculating binding energy between two systems

Regarding the calculation of binding energy of molecular absorption on graphene, for which this has been discussed before, the process of calculating $E_{AB}$ is fairly straight forward, i.e., it is ...
11
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2answers
164 views

Converting adsorption binding energy to absolute temperature

The binding interaction energy during the adsorption of system B on system A can give an idea if the interaction is favorable (negative value) or unfavorable (positive value). Also, the absolute value ...
10
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3answers
163 views

How I can analyze and present docking results?

I did a docking job and got a score of -5.69 kcal/mol and a value for MM-GBSA of -60 kcal/mol. I should analyze these results for my thesis but do not know how to comment on them. Does anyone have ...
12
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2answers
175 views

What are the scientific justifications of the binding energy equation?

There are many problems where we want to calculate the binding energy between two systems. Normally, we have a system A, adsorbent (a surface, a nanotube, a protein, etc.), that interact with a system ...