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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…
Prewriting is the process of generating and organising ideas before a first draft. It consists of a combination of informal, iterative, and semi-structured strategies such as visual diagramming, which poses a challenge for collaborating…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
Nonlinear mixed effects modeling is a powerful tool when analyzing data from several entities in an experiment. In this paper, we present NLMEModeling, a package for mixed effects modeling in Wolfram Mathematica. NLMEModeling supports mixed…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extraction of coarse-grained, macroscopic information from…
AsaPy is a custom-made Python library designed to simplify and optimize the analysis of aerospace simulation data. Instead of introducing new methodologies, it excels in combining various established techniques, creating a unified,…
Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
As scientific work becomes more computational and data intensive, research processes and results become more difficult to interpret and reproduce. In this poster, we show how the Jupyter notebook, a tool originally designed as a free…
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Scientific workflows facilitate computational, data manipulation, and sometimes visualization steps for scientific data analysis. They are vital for reproducing and validating experiments, usually involving computational steps in scientific…
We report a case study where an existing materials science course was modified to include numerical simulation projects on the micromagnetic behavior of materials. The Ubermag micromagnetic simulation software package is used in order to…
AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials,…
We present PolyMorph, a lightweight standalone C++ program that extends its predecessor PolyHoop by a finite-difference solver for multi-component reaction-advection-diffusion equations. PolyMorph simulates two integral parts of tissue…
With the establishment of machine learning (ML) techniques in the scientific community, the construction of ML potential energy surfaces (ML-PES) has become a standard process in physics and chemistry. So far, improvements in the…
A conventional study of fluid simulation involves different stages including conception, simulation, visualization, and analysis tasks. It is, therefore, necessary to switch between different software and interactive contexts which implies…