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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How does dimer and monomer zero point energy affect dissociation energy?

This paper by Xinchuan Huang et al. gives a calculation for the dissociation energy of a water dimer. The electronic dissociation energy (what they call $D_e$) is around 21 kJ/mol, and this is ...
Alex I's user avatar
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6 votes
1 answer
331 views

Which is better for binding energies: DFT-D3 or RI-MP2?

I am trying to calculate the binding energy of a small molecule with an underlying surface. I have used B3LYP-D3BJ (as implemented in ORCA) at def2-TZVP basis set to optimize the geometry of the VdW ...
Hemanth Haridas's user avatar
1 vote
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Adaptive Biasing Force Simulations in NAMD [closed]

I have performed an ABF simulation to investigate the binding of a small molecule with a 2D surface using NAMD. The initial simulation was for a scan window of 3 to 15 angstroms of z-projected ...
Hemanth Haridas's user avatar
4 votes
1 answer
256 views

VASP with VDW dispersion corrections for a large system

I have been trying to find the binding energy of a water molecule with a crystalline silica slab and want to use vasp. whenever I try to use vasp for this purpose i get this error. Also, can someone ...
Xdrake's user avatar
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7 votes
1 answer
223 views

Spin-Orbit coupling effects in topological insulator Bi2Se3

I'm currently trying to understand this paper explaining the origin of band inversion in the topological insulator Bi2Se3. In Fig. 2 (see below) they explain by means of 4 steps how certain atomic (...
Mika R.'s user avatar
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3 votes
0 answers
101 views

Is there a way to estimate the energy of desorption of an adsorbed molecule? [closed]

I'm studying the adsorption of several molecules in metal organic frameworks (MOFs) using both experimental and computational methods. Experimetally I can easily obtain the temperature at which a ...
manuelpb's user avatar
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7 votes
1 answer
100 views

Is the HOMO energy obtained from GW calculation always a value relative to the vacuum energy (-Ip)?

Aim: I want to obtain a reasonably accurate ionization energy (or work function in other terms) for a 2-dimensional hBN monolayer. The exact material does not matter much respective to the question, ...
Neinstein's user avatar
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3 votes
1 answer
403 views

Where can I find this formula?

I found this source code written by someone: ...
user366312's user avatar
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8 votes
1 answer
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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, ...
S R Maiti's user avatar
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11 votes
2 answers
1k 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) ...
littleworth's user avatar
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6 votes
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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 ...
Barbaud Julien's user avatar
8 votes
1 answer
1k 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 ...
M_Fisher's user avatar
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6 votes
0 answers
201 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 ...
Andrea's user avatar
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12 votes
1 answer
658 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 ...
Jack's user avatar
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9 votes
1 answer
98 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. ...
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7 votes
1 answer
551 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)....
BND's user avatar
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8 votes
2 answers
355 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 ...
BND's user avatar
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18 votes
2 answers
603 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 ...
Shahid Sattar's user avatar
12 votes
2 answers
372 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 ...
Camps's user avatar
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12 votes
3 answers
4k 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 ...
Giu's user avatar
  • 477
13 votes
2 answers
1k 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 ...
Camps's user avatar
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