Related papers: MDcraft -- a modern molecular dynamics simulation …
Recent advancements in protein structure determination are revolutionizing our understanding of proteins. Still, a significant gap remains in the availability of comprehensive datasets that focus on the dynamics of proteins, which are…
In this paper we announce the public release of a massively-parallel, GPU-accelerated software, which is the first to combine both coarse-grained molecular dynamics and field-theoretical simulations in one simulation package. MATILDA.FT…
The "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery…
The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is…
Supported nanoparticle catalysts are widely used in the chemical industry. Computational modeling of supported nanoparticles based on density functional theory (DFT) often involves structural searches of stable local minimum energy…
We propose the powerful integration of the Hybrid Monte Carlo (hybridMC) algorithm and Well-Tempered Metadynamics. This new algorithm, hybridMC-MetaD, enhances the flexibility and applicability of metadynamics by allowing for the…
MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…
Large-scale atomistic simulations are essential to bridge computational materials and chemistry to realistic materials and drug discovery applications. In the past few years, rapid developments of machine learning interatomic potentials…
High-performance computing platforms are becoming more and more heterogeneous, which makes it very difficult for researchers and scientific software developers to keep up with the rapid changes on the hardware market. In this paper, the…
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…
We present the first open release of the DCA++ project, a high-performance research software framework to solve quantum many-body problems with cutting edge quantum cluster algorithms. DCA++ implements the dynamical cluster approximation…
Event generators simulate particle interactions using Monte Carlo techniques, providing the primary connection between experiment and theory in experimental high energy physics. These software packages, which are the first step in the…
Machine learning has emerged as a promising paradigm to study the quantum dissipative dynamics of open quantum systems. To facilitate the use of our recently published ML-based approaches for quantum dissipative dynamics, here we present an…
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…
The MCPlas toolbox represents a collection of MATLAB functions for the automated generation of an equation-based fluid-Poisson model for non-thermal plasmas in the multiphysics simulation software COMSOL. Following the development of the…
ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and…