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. ...
Lucas Lodeiro's user avatar
20 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 ...
Nike Dattani - No Free Time's user avatar
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}{...
Mithridates the Great's user avatar
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 ...
Saleh's user avatar
  • 271
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 ...
Greg's user avatar
  • 1,807
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 ...
Cody Aldaz's user avatar
  • 8,017
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 ...
WaterMolecule's user avatar
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 ...
Max's user avatar
  • 319
13 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 ...
Nike Dattani - No Free Time's user avatar
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 ...
Nike Dattani - No Free Time's user avatar
12 votes
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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 ...
Aditya Koneru's user avatar
12 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 ...
goGopher's user avatar
  • 123
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 ...
Camps's user avatar
  • 23.3k
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 ...
Lee-Ping Wang's user avatar
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 ...
Gumbercules's user avatar
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, ...
Nike Dattani - No Free Time's user avatar
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, ...
Camps's user avatar
  • 23.3k
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 ...
Camps's user avatar
  • 23.3k
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 ...
Kristof Bal's user avatar
  • 1,341
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 ...
Geoff Hutchison's user avatar
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 ...
B. Kelly's user avatar
  • 4,366
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 ...
Pranav kumar's user avatar
  • 4,108
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 $\ce{Zr-Ni-Sn}$....
Pranav kumar's user avatar
  • 4,108
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 ...
Max's user avatar
  • 319
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 ...
WaterMolecule's user avatar
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 ...
Camps's user avatar
  • 23.3k
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 ...
S R Maiti's user avatar
  • 6,851
6 votes
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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 ...
Shern Ren Tee's user avatar

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