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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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 ...
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Adaptive Biasing Force Simulations in NAMD
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 ...
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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 ...
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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 (...
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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 ...
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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, ...
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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, ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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. ...
user1263
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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)....
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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