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
votes
1answer
122 views

How can I find the binding energy for exciton (optical gap) with VASP?

What is the best way to find the binding energy for exciton using VASP? I have heard about the method of calculating it through the dielectric tensor with local ...
6
votes
0answers
64 views

Unresolvable inconsistency between charge and multiplicity and orbital occupancies. Error while Distance Scan [closed]

I get the message mentioned in the title after a distance scan with a Gaussian calculation. I have bound a gold atom to a carbon in the pyridine ring and now pull this further and further out with a ...
11
votes
1answer
95 views

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
votes
1answer
56 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
votes
1answer
155 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
votes
2answers
117 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
votes
2answers
145 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 ...
12
votes
2answers
183 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
votes
3answers
223 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 ...
13
votes
2answers
198 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 ...