Related papers: Extrapolating molecular dynamics simulations to ze…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
We implement the statistically sound G-JF thermostat for Langevin Dynamics simulations into the ESPREesSo molecular package for large-scale simulations of soft matter systems. The implemented integration method is tested against the…
The melting point of a material constitutes a pivotal property with profound implications across various disciplines of science, engineering, and technology. Recent advancements in machine learning potentials have revolutionized the field,…
We derive unconditionally stable and convergent variable-step BDF2 scheme for solving the MBE model with slope selection. The discrete orthogonal convolution kernels of the variable-step BDF2 method is commonly utilized recently for solving…
The method of choice for integrating the equations of motion of the general N-body problem has been to use an individual time step scheme. For the sake of efficiency, block time steps have been the most popular, where all time step sizes…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
The statistics of steps and dwell times in reversible molecular motors differ from those of cycle completion in enzyme kinetics. The reason is that a step is only one of several transitions in the mechanochemical cycle. As a result,…
Phase separation plays an role in determining the self-assembly of biological and soft-matter systems. In biological systems, liquid-liquid phase separation inside a cell leads to the formation of various macromolecular aggregates. The…
Cryogenic buffer gas cells have been a workhorse for the cooling of molecules in the last decades. The straightforward sympathetic cooling principle makes them applicable to a huge variety of different species. Notwithstanding this success,…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
A new time discretization scheme for the numerical simulation of two-phase flow governed by a thermodynamically consistent diffuse interface model is presented. The scheme is consistent in the sense that it allows for a discrete in time…
We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…
Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
The choice of a time integration scheme is a crucial aspect of any transient fluid simulation, and Smoothed-Particle Hydrodynamics (SPH) is no exception. The influence of the time integration scheme on energy balance is here addressed. To…
We show through a nonlinear Fokker-Planck formalism, and confirm by molecular dynamics simulations, that the overdamped motion of interacting particles at T=0, where T is the temperature of a thermal bath connected to the system, can be…
In molecular simulations, one of the most difficult points is to track the real dynamics of many-body systems from the first principle. The present study shows that step-size dependences have an unexpected effect on simulation results, even…
We present a new time-stepping criterion for N-body simulations that is based on the true dynamical time of a particle. This allows us to follow the orbits of particles correctly in all environments since it has better adaptivity than…