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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…
Modern observations of the interstellar medium (ISM) in galaxies detect a variety of atomic and molecular species. The goal is to connect these observations to the astrochemical properties of the ISM. 3D hydro-chemical simulations attempt…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
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…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
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…
Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…
Molecular dynamics simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous…
The knowledge of the local electronic structure of heterogeneous solid materials is crucial for understanding their electronic, magnetic, transport, optical, and other properties. VASP, one of the mostly used packages for density-functional…