Sample codes for my CUDA programming book
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Dec 14, 2025 - Cuda
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molecular-dynamics-simulation
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.
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MDAnalysis is a Python library to analyze molecular dynamics simulations.
python science molecular-dynamics computational-chemistry molecular-simulation molecular-dynamics-simulation trajectory-analysis mdanalysis
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Dec 15, 2025 - Python
Graphics Processing Units Molecular Dynamics
machine-learning neural-network simulation gpu cuda molecular-dynamics neuroevolution high-performance-computing molecular-dynamics-simulation phonon physics-simulation natural-evolution-strategies heat-transport gpumd machine-learning-potential
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Dec 14, 2025 - Cuda
Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Code" button, or follow the "Releases" link below.
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Oct 25, 2025 - Fortran
Sample codes for my book on molecular dynamics simulation
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Dec 10, 2025 - Jupyter Notebook
RadonPy is a Python library to automate physical property calculations for polymer informatics.
data-science polymer simulation modeling molecular-dynamics molecular-dynamics-simulation lammps rdkit materials-science materials-informatics data-driven-design polymer-simulation high-throughput-computing psi4 polymer-informatics
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Dec 8, 2025 - Python
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
python molecular-dynamics openmm molecular-dynamics-simulation drug-discovery free-energy free-energy-perturbation alchemical-free-energy-calculations mskcc alchemical
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Jul 6, 2023 - Python
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
python monte-carlo molecular-dynamics solubility molecular-dynamics-simulation drug-discovery docking ligand-screening teaching-materials educational-software
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Mar 11, 2025 - Jupyter Notebook
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
automatic-differentiation molecular-dynamics molecular-dynamics-simulation geometric-algorithms algorithmic-differentiation differentiable-programming symbolic-integration scientific-machine-learning sciml
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Nov 25, 2025 - Julia
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
json-schema molecular-dynamics computational-biology computational-chemistry molecular-simulation computational-physics molecular-dynamics-simulation file-converter quantum-chemistry file-conversion quantum-chemistry-programs data-parsing molecular-mechanics input-output file-format-converter file-formats theoretical-chemistry file-format-library quantum-chemistry-packages molecular-electronic-structure
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Dec 14, 2025 - Python
Molecular dynamics simulation software
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Jun 25, 2023 - C
LAMMPS tutorials for both beginners and advanced users
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Oct 2, 2025 - Shell
An open source Python framework for transition interface and path sampling calculations.
monte-carlo molecular-dynamics molecular-dynamics-simulation molecular-modeling biomolecular-simulation path-sampling
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Dec 15, 2025 - Python
Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.
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Dec 1, 2025 - Julia
Monte Carlo and Molecular Dynamics Simulation Package
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Jul 20, 2024 - C++
Fully automated high-throughput MD pipeline
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Sep 1, 2025 - Python
molecular-dynamics molecular-dynamics-simulation monte-carlo-simulation opls alchemical-free-energy-calculations opls-aa cm1a
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Dec 18, 2024 - Python
Real time molecular dynamics in the browser using LAMMPS
visualization webgl molecular-dynamics webassembly molecular-simulation molecular-dynamics-simulation lammps atomistic-simulations
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Dec 15, 2025 - C++
A solar system simulator with Verlet, using OpenGL for displaying.
opengl lightning simulation shaders xml physics planet molecular-dynamics moon computational-physics molecular-dynamics-simulation solar gravitation glm physics-simulation solarsystem mfc shadow 3d 3d-graphics
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Nov 19, 2025 - C++
PyRod - Tracing water molecules in molecular dynamics simulations
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Oct 31, 2025 - Python
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