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15 votes
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What are the scientific justifications of the binding energy equation?

The justification is simple and comes from a very fundamental law of thermodynamics: Internal energy is a complete differential form and is independent of intermediate states and only depends on start ...
Mithridates the Great's user avatar
14 votes

Converting adsorption binding energy to absolute temperature

If I want to break a Li$_2$ molecule (i.e. remove atom A from atom B), one way to do it is by shining a laser on it such that the frequency ($\nu$) or energy ($h\nu$) corresponds to the difference ...
Nike Dattani - No Free Time's user avatar
13 votes
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How I can analyze and present docking results?

You can analyze your docking results in two ways. First way is looking for the score function your program uses. For some score functions, lower value indicates better interactions and for others, ...
Camps's user avatar
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12 votes

Calculating binding energy between two systems

The binding energy is defined in terms of the relaxed structures: it is the minimum energy required to disassemble a system of particles into separate parts. Mathematically $E_{\rm bind} = E(A)+E(B)-E(...
Susi Lehtola's user avatar
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12 votes
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How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

Which is more appropriate for the binding energy? Neither. Obi-Wan voice: "These are not the energies you're looking for." If I understand your goal, you're trying to compare two ligands and ...
dwhswenson's user avatar
  • 2,057
10 votes

Calculating binding energy between two systems

As Susi notes, the rearrangements of the $\ce{A}$ and $\ce{B}$ fragments are a part of the binding process, and so it is natural to include this "rearrangement energy" into the overall ...
Tyberius's user avatar
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9 votes

What are the scientific justifications of the binding energy equation?

In general, a system composed of $K$ interacting subsystems have a potential energy at a specific configuration of its parts. For instance, a system of $M$ nuclei and $N$ electrons can be separated ...
Verktaj's user avatar
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8 votes

How I can analyze and present docking results?

Docking results can be analyzed in a number of ways by looking at various geometric parameters, such as a distances, angles and dihedrals. These are then typically compared against "ideal" values, ...
kskinnerx16's user avatar
  • 1,546
8 votes

Converting adsorption binding energy to absolute temperature

A more approximate but sometimes easier approach than the one of Nike Dattani might be to calculate an artificial reaction coordinate of separating the two systems. This can be done manually or by ...
patrickmelix's user avatar
8 votes
Accepted

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

Summary of my recommendation If my choices are B3LYP-D3 and RI-MP2 for calculating a binding energy at a molecule whose geometry was optimized with B3LYP-D3, I would find it easier to justify using ...
Nike Dattani - No Free Time's user avatar
8 votes
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Where can I find this formula?

The formulas that the code is using can be directly read off from the code. The code simulates a two-dimensional periodic box, and calculates the distance of each atom to each other atom, namely d. If ...
wzkchem5's user avatar
  • 9,670
7 votes

What do size-extensivity and size-consistency mean?

Size-consistency: Your description is correct. $E_{AB}(r=\infty) = E_A + E_B$. Size-extensivity: I explained this in my answer "Constraint #13: Size-Extensivity" to the question asking for ...
Nike Dattani - No Free Time's user avatar
7 votes
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How can I find the binding energy for exciton (optical gap) with VASP?

The model you are describing corresponds to a Wannier-Mott exciton and the binding energy is approximated by: $$ \tag{1} E_{\mathrm{B}}=\frac{\mu}{\epsilon^2_{\infty}}R, $$ where $\mu$ is the reduced ...
ProfM's user avatar
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7 votes
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Binding energy calculation for Zn atom on armchair graphene slab?

As mentioned by @Camps in the comments, the Zn reference used in the paper is almost certainly that of an isolated Zn atom in the gas phase. If I understand correctly from briefly scanning the paper, ...
leopold.talirz's user avatar
7 votes
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Is it required to sample the full reaction coordinate in umbrella sampling?

The short answer is: yes you need to sample the whole reaction coordinate if you want accurate free energy values. If you are simply interested in qualitative behaviour, then you might (key word being ...
Godzilla's user avatar
  • 1,938
6 votes

Docked pose and energy minimization

One way these calculations are performed is using MD and implicit solvent calculations. The general procedure for these simulations are: Perform simulations and get frames Perform implicit solvent ...
kskinnerx16's user avatar
  • 1,546
5 votes

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

Just complementing the @dwhswenson answer, when studying ligand/protein binding process, there is no best energy to look for. In the binding process there are several mechanism that will influence it. ...
Camps's user avatar
  • 23.6k
5 votes

Spin-Orbit coupling effects in topological insulator Bi2Se3

Welcome to MMSE! That's an interesting question! At first the "crossing" of energy levels seemed peculiar to me, but when I look at the energy levels for Se and for Bi separately, everything ...
Nike Dattani - No Free Time's user avatar
4 votes
Accepted

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

In the meantime, Daniele Varsano answered me on the Yambo forum. I quote him below: In Yambo, the zero of the energy is set at the valence band maximum (VBM). The GW will give you the correction to ...
3 votes

How I can analyze and present docking results?

A good way to proceed is to use a control in your experiment as with modelling experiment in general. You can, for example, use the co-crystalized ligand or a well-know inhibitor (something ...
BND's user avatar
  • 1,341
3 votes

What is exfoliation energy per unit area?

Unfortunately, these appear to be the same quantity (a somewhat disappointing answer). They only differ in units, you can convert between the atomwise and area based units by simply calculating the ...
Tristan Maxson's user avatar
2 votes

VASP with VDW dispersion corrections for a large system

It was killed, this indicates something externally killed it. Likely a manager for the cluster preventing you from running long jobs on the front end or the job simply ran out of time. Simply submit ...
Tristan Maxson's user avatar
2 votes

Docked pose and energy minimization

Absolutely not. You only need that your input structure geometry is ok (no atomic clash, all valence ok, etc ). Using DFT or Molecular Dynamics to optimize the geometry pre docking is a waste of time. ...
Camps's user avatar
  • 23.6k

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