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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/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/aslozada/coor2graph

COOR2GRAPH - This software converts a molecular dynamics trajectory in GRO format into an adjacency matrix. The adjacency matrix is called by networkx python library.

graphs ising-model-2d lennard-jones-fluid molecular-dynamics monte-carlo-simulation periodic-boundary-conditions

Last synced: 07 Jan 2025

https://github.com/snapex2409/komd

Small MD framework

kokkos md molecular-dynamics simulation

Last synced: 20 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

https://github.com/smahala02/atomistic-simulation

This project demonstrates how atomistic simulations are used to predict and analyze the behavior of atoms and molecules, providing detailed tutorials and simulations in a Jupyter Notebook.

atomistic-simulation computational-chemistry materials-science molecular-dynamics physics python

Last synced: 30 Dec 2024

https://github.com/jackrekirby/accord2

AcCoRD 2: A redesigned Actor-based Communication via Reaction-Diffusion simulator in C++.

biochemistry cpp matlab modelling molecular-dynamics

Last synced: 08 Feb 2025

https://github.com/simongravelle/vmd-tutorial

Generate good-looking images and movies with VMD

guide lammps molecular-dynamics tutorials vmd

Last synced: 01 Jan 2025

https://github.com/samuelhoover/gromacs-tutorials

GROMACS tutorials and exercises.

all-atoms gromacs molecular-dynamics

Last synced: 07 Jan 2025

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 293 Awesome-Graph-Research-ICML2024 295 awesome-ai4molconformation-md 259
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 20 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