26
votes
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What is the appropriate way of determining a value for the Hubbard-like potential U for LDA+U / GGA+U calculations?
This is a bit late, but I would say the short answer to your direct question is: technically no, there is no "standard" reliable way, since there are several approaches to determining U self-...
- 3,191
23
votes
In molecular mechanics, how are van der Waals forces modelled?
Additional to Alone Programmer's answer. The Lennard-Jones Potential (LJ 12-6) is the standard, but is not unique, in some cases the factor of 6 is changed to 8 to simulate better the hydrogen bonds.
...
- 331
20
votes
In molecular mechanics, how are van der Waals forces modelled?
You are looking for Lennard-Jones potential. Basically, the interatomic interaction is modeled by this formula:
$$U(r) = 4 \epsilon \Bigg [ \Big ( \frac{\sigma}{r} \Big )^{12} - \Big ( \frac{\sigma}{...
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20
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In molecular mechanics, how are van der Waals forces modelled?
First I will try to directly answer this question:
In terms of energy, how are van der Waals forces modelled (are there
formulas that govern these)?
The most common way to model the potential ...
18
votes
What is the appropriate way of determining a value for the Hubbard-like potential U for LDA+U / GGA+U calculations?
You can calculate U in an ab initio way via linear response theory, for instance. See an example here. However, there is no guarantee that a linear response U value is empirically ideal. That is part ...
- 7,401
15
votes
What is the appropriate way of determining a value for the Hubbard-like potential U for LDA+U / GGA+U calculations?
The answer is based on Chapter 1 - The DFT+U: Approaches, Accuracy, and Applications from the book Density Functional Calculations: Recent Progresses of Theory and Application
For practical ...
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14
votes
How do you incorporate hydrogen bonding into molecular simulations?
The short answer is that, while hydrogen bonds do have some covalent character, you can mimic that covalent character by increasing the electrostatic term. For example you can specify point charges to ...
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14
votes
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How does one compute the boiling point of a liquid made of a particular molecule?
I would like to start off by saying this is first and foremost a thermodynamic problem.
Secondly, and as a result of thermodynamics, refer to Gibbs Phase Rule which says
\begin{equation}
F = C - P + 2
...
- 4,406
14
votes
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Simulating breaking bonds in molecular dynamics
The quadratic potential is the simplest possible model for a bond. You can derive it by considering the Taylor expansion of the potential around the natural bond length
$V(r - r_0) = V(r_0) + \frac{d ...
- 928
11
votes
Simulating breaking bonds in molecular dynamics
Very short answer: No, classical molecular dynamics cannot break bonds.
The potential you showed is the most common form of bond, the harmonic potential a.k.a. Hookes law.
If you have ever broken a ...
- 4,406
10
votes
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How do you incorporate hydrogen bonding into molecular simulations?
The current biomolecular force fields that I'm familiar with don't include any special energy terms for hydrogen bonds. Typically, hydrogen atoms that are capable of hydrogen bonding have very small ...
- 1,951
10
votes
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Benchmarking data for Ewald summation algorithms
I have looked for a similar set of benchmarks and haven't found one, unfortunately. Hopefully the data referred to in the comments comes through!
In the meantime, I have an MIT-licensed implementation ...
- 1,893
9
votes
What are the different ways of calculating dispersion constants?
2007 (Becke & Johnson): XDM
XDM stands for "exchange-hole dipole moment" which is a model introduced by Becke and Johnson in 2007 for calculating dispersion constants. The formulas are ...
9
votes
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DFT modeling intermolecular interactions
They are included in long range type functionals. Here are some references:
S. Grimme, Semiempirical GGA-type density functional constructed with a long-range dispersion correction, J. Comput. Chem. ...
- 24k
8
votes
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Empirically determining thermostat damping factor
To the best of my knowledge, there is no universal or even near-universal heuristic for what the time constant should be. The only rule of thumb I have encountered is that the time constant should be ...
- 1,658
8
votes
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Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?
Changing the force field parameters is not a good/recommended approach. This is due to the high number of parameters you have to know. Many of them, you cannot obtain from experimental data. Instead, ...
- 24k
7
votes
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Rule-of-thumb for Morse potential cutoff in molecular dynamics?
Since you are referring to "the Morse potential", I assume you mean to use it for modeling van der Waals interactions?
If not, please ignore this answer and consider updating your question to include ...
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7
votes
Can the NCI (noncovalent interaction) index be generated starting with psi4?
If you call wfn.compute_hessian(), Psi4 tries to compute the nuclear Hessian which is indeed not implemented for most methods.
Calling ...
- 20k
7
votes
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Can the NCI (noncovalent interaction) index be generated starting with psi4?
Not a full answer of an alternative program, but just collecting the conclusions from the comments along with some additional suggestions.
It appears that ...
- 15.7k
7
votes
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Which equation makes it possible to calculate the forces of attraction between a surface and molecules?
The long-range (non-chemical) interaction between a neutral molecule and a surface is dominated by van der Waals interactions. The simplest model you could use for this is a Lennard-Jones potential, ...
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votes
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What's a quick way to get a molecular bond length using a Newtonian model?
The quality of force fields depends a lot on the parameters.
For example, if I use Avogadro and draw out O=O and optimize using the default (MMFF94) I get an O-O distance of 1.282 Å. If I optimize ...
- 9,375
6
votes
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Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?
I think the effect of larger cutoffs will not affect your simulation. Shorter cutoffs will be more problematic and can see artifacts than the larger cutoffs. Even if you have larger cutoffs, the ...
- 1,426
6
votes
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How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?
Following Tyberius's suggestion, I now turn my comment into an answer.
As always, the most reliable way of estimating the effect of the dispersion correction is to actually do two simulations, one ...
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6
votes
Which equation makes it possible to calculate the forces of attraction between a surface and molecules?
The Schrödinger (or relativistic Dirac) equation is what essentially determine the interaction, and there are many free and open source programs that can perform such calculations; a recent listing ...
- 20k
5
votes
What are the different ways of calculating dispersion constants?
2009 (Tkatchenko−Scheffler) TS
The Tkatchenko−Scheffler model for van der Waals interactions (vdW) defines the $C_6^{AB}$ parameters in an ab-initio fashion. In TS model the vdW energy $E_{vdw}$ is ...
- 2,352
5
votes
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Should I add vdW interaction to estimate chemical potential of metallic elements?
Short version
If the $\text{LiCoO}_2$ is computed with van der Waals included, so should everything else.
Long version
This seems more of a thermodynamics question than a simulations question given ...
- 1,658
5
votes
Is it okay to use semi-empirical methods to optimize structures if I perform high-level energy calculations?
I generally try to use the most accurate methods that my resources will allow me to use, within a reasonable budget for the desired accuracy.
If you're interested in 20 water molecules or 60 atoms (...
5
votes
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DFPT vs analytical nuclear gradient
These are not the same quantity. The gradient of the energy with respect to the position $\vec{R}_i=(x_i,y_i,z_i)$ of atom $i$ gives the force, $\vec{F}_i$, acting on that atom,
$$
\vec{F}_i=-\left(\...
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4
votes
Simulating breaking bonds in molecular dynamics
You can do something with Lennard-Jones potentials instead of harmonic ones. I know this has been done for Coarse-Grained MD simulations using Go-Martini models as in https://pubs.acs.org/doi/abs/10....
- 879
4
votes
Energy balance in a molecular dynamics simulation with ghost atoms and periodic boundary conditions?
Newton's Third Law (N3L) is respected by force pairs in practically all molecular dynamics (MD) simulations, so where packages include a newton option (as LAMMPS ...
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