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Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
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…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
Machine-learned interatomic potentials have revolutionized molecular dynamics simulations by providing quantum-mechanical accuracy at empirical-potential speeds. The graphics processing unit molecular dynamics (GPUMD) package, featuring the…
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…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
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…
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Molecular visualization software has long supported research and education in chemical and structural sciences, but consumer devices constrained to 2D inputs and outputs pose two major challenges: they poorly convey 3D nature, and 3D…
The Collective Variables Dashboard is a software tool for real-time, seamless exploration of molecular structures and trajectories in a customizable space of collective variables. The Dashboard arises from the integration of the Collective…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…
Molecular optimization is a key challenge in drug discovery and material science domain, involving the design of molecules with desired properties. Existing methods focus predominantly on single-property optimization, necessitating…
VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
There are many ways to represent a molecule as input to a machine learning model and each is associated with loss and retention of certain kinds of information. In the interest of preserving three-dimensional spatial information, including…
Artificial Intelligence (AI)-driven material design has been attracting great attentions as a groundbreaking technology across a wide spectrum of industries. Molecular design is particularly important owing to its broad application domains…
The OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format…
We present a web-based software tool, the Virtual Quantum Optics Laboratory (VQOL), that may be used for designing and executing realistic simulations of quantum optics experiments. A graphical user interface allows one to rapidly build and…