Related papers: Discrete Molecular Dynamics
A recent article in J. Chem. Phys. argues that the two algorithms, the velocity-Verlet, and position-Verlet integrators, commonly used in Molecular Dynamics (MD) simulations, are different \cite{Ni2024}. But not only are the two algorithms…
In 1687 Isaac Newton published PHILOSOPHI\AE \ NATURALIS PRINCIPIA MATHEMATICA, where the classical analytic dynamics was formulated. But Newton also formulated a discrete dynamics, which is the central difference algorithm, known as the…
Almost all Molecular Dynamics (MD) simulations are discrete dynamics with Newton's algorithm first published in 1687, and much later by L. Verlet in 1967. Discrete Newtonian dynamics has the same qualities as Newton's classical analytic…
For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exists a shadow Hamiltonian $\tilde{H}$ with energy $\tilde{E}(h)$, for which the discrete particle positions lie on…
Simulations of objects with classical dynamics are in fact a particular version of discrete dynamics since almost all the classical dynamics simulations in natural science are performed with the use of the simple ''Leapfrog" or ''Verlet"…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
A set of algorithms is presented for efficient numerical calculation of the time evolution of classical dynamical systems. Starting with a first approximation for solving the differential equations that has a "reversible" character, we show…
We study classical Hamiltonian systems in which the intrinsic proper time evolution parameter is related through a probability distribution to the physical time, which is assumed to be discrete. - This is motivated by the ``timeless''…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We study classical Hamiltonian systems in which the intrinsic proper time evolution parameter is related through a probability distribution to the physical time, which is assumed to be discrete. In this way, a physical clock with discrete…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found,…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…
The dynamics of the classical Lorenz system is well studied in $1963$ by E. N. Lorenz. Later on, there have been an extensive studies on the classical Lorenz system with the complex variables and the discrete time Lorenz system with real…
Modifying the discrete mechanics proposed by T.D. Lee, we construct a class of discrete classical Hamiltonian systems, in which time is one of the dynamical variables. This includes a toy model of time machines which can travel forward and…
The equations of classical mechanics can be used to model the time evolution of countless physical systems, from the astrophysical to the atomic scale. Accurate numerical integration requires small time steps, which limits the computational…
Discrete gradients (DG) or more exactly discrete gradient methods are time integration schemes that are custom-built to preserve first integrals or Lyapunov functions of a given ordinary differential equation (ODE). In conservative…
Classical molecular dynamics simulations are based on solving Newton's equations of motion. Using a small timestep, numerical integrators such as Verlet generate trajectories of particles as solutions to Newton's equations. We introduce…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…