23

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. Also, there is the Buckingham potential, where the repulsion part ($r^{12}$ term) is modified to the exponential term. But the attractive long-range term ($r^{...


20

You are looking for Lennard-Jones potential. Basically, the interatomic interaction is modeled by this formula: $$U(r) = 4 \epsilon \Bigg [ \Big ( \frac{\sigma}{r} \Big )^{12} - \Big ( \frac{\sigma}{r} \Big )^{6} \Bigg ]$$ Particularly the term $r^{-6}$ in the above formula describes long-range attraction force based on van der Waals theory. Update: I'll ...


19

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 energy between two ground state (S-state) atoms that are far apart, is by the London dispersion formula: $$V(r) = -\frac{C_6}{r^6}$$ where $C_6$ depends on the ...


13

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 paper on the work can be found here https://pubs.acs.org/doi/10.1021/jz500737m From the GitHub page it says "The purpose of ForceBalance is to create ...


13

I am afraid I can't be of much help regarding the QM part of your simulation, but I can give some thoughts on the MM part. In short: you should use the cutoff that was used to validate your force field. While a proper ab initio method is expected to improve with a longer cutoff, this is not necessarily true for force fields. The reason for that is that force ...


11

Very interesting question! The LJ potential is quite benign in that it has a $r^{-6}$ decay, which is pretty rapid. However, MD codes typically go a bit farther than a straightaway truncation at $r_{\rm max}$, but instead also apply an analytical correction for the region $[r_{\rm max},\infty)$. The analytical correction for the cut-off can be justified by ...


8

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 text, XML files or objects in code), the possible values or ranges of parameters, the software that runs simulations using the force field, the experimental ...


7

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 calculators, including some DFT options.


7

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 what kind of potential you are modeling using the Morse potential. If so, here is my answer: There is a rule of thumb based on experience and a lot of ...


6

You iterate through the bond, angle, torsion, etc. contributions and sum the gradients on each atom. When we were implementing these for Open Babel, we found a very nice dissertation which gave some insight into MMFF94 gradients: Dr. Andreas Moll BALLView : a molecular viewer and modeling tool Bonds - harmonic potential leads to, e.g.: $$ S_{i j} \frac{\hat{...


5

GULP GULP (General Utility Lattice Program) uses specific forcefields for different type of systems and it is designed to work with periodic conditions. Also, it has defined several type of potential models for two-body (Buckingham, Lennard-Jones, Morse, etc.), three-body (Three-body harmonic, Axilrod-Teller, Stillinger-Weber, etc.), four-body, six-body and ...


5

The charge-charge interactions are only including things which aren't "bonded", this includes angles, and sometimes 1,4 Torsions. This is because the electrostatic interaction is already included in the parameterization of those potentials. So in your data, this is why we see charge-charge parameters between carbon and a bunch of hydrogens, because ...


5

Typically, force evaluation happens in Cartesian coordinates regardless of the approach (QM or MM). In QM codes the forces may then be projected into internal coordinates, which in turn is usually dependent on the geometry, see e.g. J. Chem. Phys. 110, 4986 (1999); even though this carries some cost, it is more than offset by the savings in fewer QM ...


Only top voted, non community-wiki answers of a minimum length are eligible