Related papers: Molecular Dynamics Simulations of Active Matter us…
Molecular dynamics simulations have emerged as a fundamental instrument for studying biomolecules. At the same time, it is desirable to perform simulations of a collection of particles under various conditions in which the molecules can…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
Since its inception in 1995, LAMMPS has grown to be a world-class molecular dynamics code, with thousands of users, over one million lines of code, and multi-scale simulation capabilities. We discuss how LAMMPS has adapted to the modern…
The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
Condensed Matter Physics (CMP) seeks to understand the microscopic interactions of matter at the quantum and atomistic levels, and describes how these interactions result in both mesoscopic and macroscopic properties. CMP overlaps with many…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Granular materials are of critical interest to many robotic tasks in planetary science, construction, and manufacturing. However, the dynamics of granular materials are complex and often computationally very expensive to simulate. We…
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded…
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,…
While machine learning approaches have been successfully used to represent interatomic potentials, their speed has typically lagged behind conventional formalisms. This is often due to the complexity of the structural fingerprints used to…