Related papers: A concise introduction to molecular dynamics simul…
We have investigated by molecular dynamics method the influence of a finite number of particles used in computer simulations on fluctuations of thermodynamic properties. As a case study, we used the two-dimensional Lennard-Jones system. 2D…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
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…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
Monads are a popular tool for the working functional programmer to structure effectful computations. This paper presents polymonads, a generalization of monads. Polymonads give the familiar monadic bind the more general type forall a,b. L a…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
A Molecular Dynamics (MD) study of static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modelled by the classical pair potential proposed by Oeffner and Elliott (OE)…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
Molecular Dynamics (MD) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…