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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/matsunagalab/md_inputs

Place of learning OpenMM

molecular-dynamics openmm

Last synced: 19 Jan 2025

https://github.com/toruniina/rustymill

MD toolbox written in rust

molecular-dynamics pdb rust science

Last synced: 08 Dec 2024

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 256
Molecular Dynamics Categories
GNN Theories 112 Interatomic Potentials (ML-IAP) 78 Representation Learning 52 Scene Graphs 41 General Tools 38 Language Models 27 Simulations 22 General Chemistry 19 Representation Engineering 19 Community resources 19 Datasets 17 Reviews 17 Casual Discovery and Graphs 16 Molecular Dynamics 16 Generative Models 15 GNN Applications 13 Universal Potentials 13 Mathematical tools 13 Graphs and Molecules 11 Density functional theory (ML-DFT) 11