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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7
votes
1answer
184 views

What do size-extensivity and size-consistency mean?

I have heard both terms in various lectures and books on quantum chemistry, however, I have not found a proper explanation of them. As I understand now, size consistency of a method means for example, ...
10
votes
2answers
254 views

How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

I was performing MD simulation for protein-ligand complex following GROMACS tutorial. I compared the energy of two ligands (S1 and S2) to a protein, using GROMACS LJ-SR (Lennard-Jones Short Range) ...
5
votes
0answers
67 views

Apparent conservation of potential energy in NPT simulation?

I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
8
votes
1answer
238 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
104 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
112 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
64 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
209 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
133 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
160 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
195 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
274 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
240 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 ...