24
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.
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21
votes
Accepted
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 ...
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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17
votes
Machine learning interatomic potentials for molecular dynamic simulations: are they good?
Before talking about the pros and cons of ML-potentials, there is a huge conceptual difference between empirical- and ML-potential that needs to be clarified.
In empirical potentials, one uses data ...
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17
votes
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Machine learning interatomic potentials for molecular dynamic simulations: are they good?
(Expanding my comment into an answer)
When ML-based forcefields are compared to classical forcefield directly, I think we miss the most important points. ML-based models have several advantages:
They ...
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16
votes
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What is the cutting edge for open-source Force-Field generation?
ForceBalance
ForceBalance is one approach which aims at making it easier to create force fields from a combination of theoretical and experimental data. I believe it's within the OpenMM framework.
The ...
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15
votes
How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?
Lennard-Jones combining rules
Most force fields define a single σ and ε for each atom and calculate them for combinations using Lorentz-Berthelot combining rules. These rules specify a arithmetic mean ...
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14
votes
How do I simulate the interaction between two atoms?
How to proceed depends on how accurate you want the outcome. Throughout my answer I will provide blue buttons which demonstrate that there's entire tags in our community to address certain aspects of ...
14
votes
How do I simulate the interaction between two atoms?
EDIT Doing what you want is hard! You will need a full quantum mechanics based simulation. This is unlikely to be something you can build yourself at the current time.
Based on your new additions to ...
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13
votes
What are some open-source codes that can generate potentials?
There are different flavors of interatomic potentials, from the classical Lennard-Jones and Morse models to more recent machine learning models. I will limit the answer to reactive potential models ...
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12
votes
How may I calculate the bond length between two atoms?
The only proper way to do it ab initio is to calculate the energy (E) for various internuclear distances (R) and then to approximate the equilibrium bond length by choosing the distance which has the ...
12
votes
Accepted
How may I create an interatomic potential using DFT?
The following are three important aspects of any force-field fitting workflow,
Training Data: There should be DFT/experimental values that define structure, energetics, elastics or any other ...
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11
votes
How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?
My recommendation is to you look at the force-fields data from software that implement Molecular Mechanics.
One example: at the Github site from the PYMATGEN project, you can get some library ...
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11
votes
What is the cutting edge for open-source Force-Field generation?
ForceBalance
Cody is right, ForceBalance is designed for the task of generating custom force fields. Force fields have a lot of variability in their functional forms, representation of parameters (as ...
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11
votes
How do I simulate the interaction between two atoms?
Generally speaking, most work in molecular dynamics tries to simulate how actual molecules behave (i.e. quantum mechanics) and it doesn't sound like you want to go down that rabbit hole. I completely ...
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11
votes
If total energies differ across different software, how do I decide which software to use?
"how do I decide on which algorithm/software to use if the total energies are different across algorithms/software?"
You can use any algorithm or software to calculate your total energies, ...
10
votes
How do I simulate the interaction between two atoms?
In order to simulate two atom interaction, you have different path to follow.
One is to use Density Functional Theory (DFT) or ab initio, make a script where the distance of the atoms is decreasing, ...
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10
votes
Qualitatively, How do MEAM Potentials Work?
In short, it is a semi-empirical approach to atom/atom interaction for periodic systems.
It is based on the embedded atom method (EAM) idea where "the energy of a given atom is taken as one half ...
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9
votes
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How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?
Universal Lennard-Jones
In addition to the answer on combining rules, there are some "universal" Lennard-Jones parameters, published by Elliott and Akerson.
The OpenKIM project is an Open ...
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9
votes
Where to get Tersoff and SW potentials for LAMMPS
Generally, if you want to perform simulations with some force field, you will have to search the literature for published FFs tailored for your problem. The Stillinger-Weber (SW) model is very popular ...
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8
votes
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Considerations when developing ab initio based interatomic potentials for classical molecular dynamics
There is quite abit of work going on in this field right now. Take a look at what Rogers et al. are doing using MP2 to derive all aspects of a force-field. They are also working on a DFT ...
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8
votes
What are some open-source codes that can generate potentials?
My answer is based on Lammps
Creating interatomic-potential which predicts every property of different phase is a nightmare job. There are few database which is already available for inter-atomic ...
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8
votes
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Is it possible to use multiple files to define eam potential in LAMMPS?
In general, It is not recommended to mix two inter-atomic potential, Let me go through the consequences, You want to mix $\ce{Ti}$ EAM potential to $\ce{Zr-Ni-Sn}$....
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7
votes
How do I simulate the interaction between two atoms?
The simplest possible atomic simulation: a noble gas
As explained by Nike Dattani, what method you use depends on what you want to simulate and why. He gives you a good roadmap for what method to ...
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7
votes
How may I calculate the bond length between two atoms?
Unfortunately the answer to this question is much the same as your last one. What you are trying to do is hard. Very hard. Creating this would be PhD if not postdoc work and doing it well could well ...
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7
votes
Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?
I searched a lot, they always said you should do scan between two atoms and then fit with Lennard-Jones Equation, but they don't explain which atom should I select or depend on what should I select ...
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6
votes
How may I calculate the bond length between two atoms?
I don't know why you need atom-atom interactions in a sandbox game. My only guess is that you want to simulate or visualize the movement of molecules of some kind in real time. If your system is large ...
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6
votes
Accepted
Determine Forces from a Bond Angle Potential
Your first question -- writing out analytical forms for forces from potential functions -- is the hardest of the lot. For manual derivations the chain rule is often useful, and your workings already ...
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