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Molecular Dynamics

Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic “evolution” of the system.

https://github.com/kgorze/molecular-dynamics-simulator

A 2D molecular dynamics simulator that models atomic interactions using Lennard-Jones forces on a Boltzmann lattice. Currently implements an all-pairs algorithm for force calculations with visualization capabilities. This academic project aims to evolve into a 3D simulation of water and solutes.

atom-simulation cpp lennard-jones molecular-dynamics physics-simulation

Last synced: 12 Feb 2025

https://github.com/snapex2409/komd

Small MD framework

kokkos md molecular-dynamics simulation

Last synced: 20 Jan 2025

https://github.com/biodasturchi/imgs

Biodasturchi sayti uchun rasmlar bazasi

bash bioinformatics molecular-docking molecular-dynamics python

Last synced: 13 Jan 2025

https://github.com/jvsguerra/iv-cec

Análises de dinâmica molecular com a ferramenta KVFinderMD para o IV Congresso de Estudantes do CNPEM

case-study cavity-characterization cavity-detection graph-theory molecular-dynamics

Last synced: 28 Dec 2024

https://github.com/peppone98/mpro_h164n

Project of the Computational Biophysics exam @Unitn. We simulated the SARS-CoV-2 main protease Mpro with the H164N mutation in complex with two CG-376 ligands

biophysics gromacs molecular-dynamics python sars-cov-2

Last synced: 28 Dec 2024

https://github.com/reyrove/reyrove

Step into Reyrove's World, where the spirit of exploration, creativity, and innovation roam freely across the realms of textile engineering, Fortran programming, web development, and Web3.

ai artificial-intelligence blockchain cryptocurrency css fortran generative-art html javascript lammps latex molecular-dynamics nft ovito programmer reyrove web-development

Last synced: 08 Feb 2025

https://github.com/janjoswig/cs-msm

Core-set Markov-state model estimation

core-set markov-model molecular-dynamics python

Last synced: 08 Feb 2025

https://github.com/adam-maz/toolkit-for-namd

I present tools that accelerate molecular dynamics (MD) simulations using NAMD software and support the analysis of the obtained trajectories.

bash clusterization gpu-acceleration medicinal-chemistry molecular-dynamics namd python

Last synced: 22 Jan 2025

https://github.com/babaid/aaperturb

A C++ library for the creation of a large dataset of amino acid sidechain perturbations, own PDB Parser code included and some other things related.

big-data gnn molecular-dynamics perturbation-methods structural-bioinformatics

Last synced: 01 Jan 2025

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 293 Awesome-Graph-Research-ICML2024 295 awesome-ai4molconformation-md 263
Molecular Dynamics Categories
GNN Theories 112 Interatomic Potentials (ML-IAP) 78 Representation Learning 52 Scene Graphs 41 General Tools 38 Language Models 28 Simulations 22 Reviews 22 General Chemistry 19 Representation Engineering 19 Community resources 19 Datasets 17 Molecular Dynamics 16 Casual Discovery and Graphs 16 Generative Models 15 Universal Potentials 13 Mathematical tools 13 GNN Applications 13 Visualization 11 Density functional theory (ML-DFT) 11