16 votes
Accepted

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 ...
  • 7,794
16 votes
Accepted

What does "force field" mean?

What is a force field? The Wikipedia entry on this is a good resource, but I'll give my own description below. In the context of molecular dynamics (MD), a force field is one way of describing the ...
  • 1,887
15 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 ...
  • 251
15 votes
Accepted

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 ...
  • 1,658
13 votes
Accepted

What are the advantages of (semi)-empirical force fields over Machine Learning Potentials?

The answer to this question is inevitably going to be opinionated. My opinion is that there are still very good reasons to explore the development of force fields while also pursuing better ML ...
  • 2,763
12 votes

Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields

We performed some timing benchmarks as part of our recent paper, albeit not on molecular dynamics: "Assessing conformer energies using electronic structure and machine learning methods" Int ...
11 votes

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

We attempted to solve a similar problem when studying the (also highly symmetrical) $\ce{CH4}$ and $\ce{CF4}$ homo- and hetero-dimers. I found it easiest to use internal coordinates and fixed ...
  • 1,603
10 votes
Accepted

How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

Since you seem to have at least a start on automating the process of modifying the file, I will just address the other two parts of your question: the format of the ...
  • 14.3k
10 votes
Accepted

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 ...
  • 1,853
10 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 ...
10 votes

How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?

I am not a GROMACS user, but have used it once or twice during my course. As far as I can remember and understand, it is common to use different force field in MD if one simulate something solvated in ...
10 votes
Accepted

What does it mean by "transferable" in the case of a force field?

A forcefield defining the interactions of an atom is said to be transferrable if it can be successfully used in chemical simulations outside of where it was originally designed or fit. For example: ...
  • 613
9 votes
Accepted

What is the state-of-the-art in current flexible water models?

Allow me to begin with a disclaimer: what you have asked is a very contentious question among people who work on water models. I think much more contentious than it should be. Not necessarily because ...
  • 2,763
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 ...
8 votes

Limitations of pairwise additive forcefields

The Axilrod-Teller force is not a "pairwise" force but a "3-body" force whose potential has the formula: $$\tag{1} V_{ijk}= E_{0} \left( \frac{1 + 3 \cos\gamma_{i} \cos\gamma_{j} \...
  • 29.2k
8 votes
Accepted

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, ...
  • 19.3k
8 votes

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

On the fitting, I would recommend Dr. Nike Dattani's answer. You can also try some other methods such as those using neural networks. I read your discussion and find that may be you have also some ...
  • 1,084
8 votes

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

For 1D analytic potentials, I highly recommend to use my potential energy form or a slight simplification of it, which I can help you with. This is known as the Morse/Long-Range (MLR) potential and is ...
  • 29.2k
8 votes
Accepted

Finding parameters for a molecule in various forcefields

Running simulations with small molecules is one thing that I found quite difficult especially because most online guides/tutorials are focused on proteins. So, here's a rough idea of what to do: ...
  • 5,834
8 votes

What does "force field" mean?

The term's origin goes back to vector field which is a function that returns a vector for any given point in space (as in the image below on the left). We can almost "see" that such fields ...
  • 29.2k
8 votes

What software implements UFF

Many codes implement UFF, including LAMMPS, RDKit, Open Babel. A few caveats... First off, the original UFF paper is known to have typos and errors. One consistent pain point is that the angle terms ...
7 votes
Accepted

How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?

Short answer I am a regular GROMACS user. I do not think you can just easily have the total functional form "printed out" from GROMACS. However, you can obtain it from the topology file (...
7 votes

Where can I find/generate force-field parameters for common inorganic anions in water?

Any parameters are better than no parameters. Part of using a FF is checking that results make sense, so if you can find something in this bare market for anions, try it. Proof will be in the pudding. ...
  • 4,066
7 votes

Symmetry-preserving low-level structural relaxation

ASE has a FixSymmetry constraint that preserves spacegroup symmetries. It works with a variety of structure optimization algorithms. You could use LAMMPS as the engine or one of the many other ...
  • 1,853
7 votes

How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

I believe I have figured it out. For those trying to martinize their all-atom files into coarse grain representations for martini 3, use the following package: https://github.com/marrink-lab/vermouth-...
  • 423
7 votes

What does "force field" mean?

Molecular dynamics is based in Molecular Mechanics. Molecular Mechanics do many approximations in order to treat the atomic/molecular system. A good definition can be seen here: Molecular Mechanics ...
  • 19.3k
7 votes

Alternative to CGenFF for generating large ligand topology

I'd use OpenMM's openmmforcefields package, which is available on GitHub. I haven't used it extensively, but I recommended to a student in a colleague's lab and ...
6 votes
Accepted

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 ...
  • 974
6 votes

What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?

I would recommend GAFF or OPLS/A Camps has outlined the OPLS FF, so I won't elaborate very much, but to say that when using LigParGen, a nice feature is that forcefields are made for many different MD ...
  • 4,066
6 votes
Accepted

Parameterize a complex that contains Transition metal (Build Force Field)?

I think that the parametrization process is straightforward (but very hardworking!): select and use an ab initio/DFT software that works well for your metal atoms, take a look at the force field ...
  • 19.3k

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