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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…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
In the field of materials science, comprehending material properties is often hindered by the complexity of datasets originating from various sources. This study introduces the Automated Model Training (AMT) Graphical User Interface (GUI),…
The accurate prediction of protein-ligand binding affinity is important for drug discovery yet remains challenging for multi-domain proteins, where inter-domain dynamics and flexible linkers govern molecular recognition. Current geometric…
VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large numbers of particles. VPIC's…
Several visualization schemes have been developed for imaging materials at the atomic level through atom probe tomography. The main shortcoming of these tools is their inability to parallel process data using multi-core computing units to…
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…
Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures,…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
Probabilistic graphical models (PGMs) serve as a powerful framework for modeling complex systems with uncertainty and extracting valuable insights from data. However, users face challenges when applying PGMs to their problems in terms of…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
We present the VASPKIT, a command-line program that aims at providing a powerful and user-friendly interface to perform high-throughput analysis of a variety of material properties from the raw data produced by the VASP code. It consists of…
MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
A hallmark of object-oriented programming is the ability to perform computation through a set of interacting objects. A common manifestation of this style is the notion of a package, which groups a set of commonly used classes together. A…
Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various…
We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step…
Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…